Stargate Atlantis

Atlantis races against time to save team members trapped in a collapsed compound, and rescue a pregnant Teyla from Michael's clutches.

When a mysterious alien organism takes Dr. Keller as its host, Beckett and the crew desperately search for a serum to save her from the evolving intruder before it can infiltrate Atlantis.

Ronon is captured by his former friend, Tyre, and turned over to the wraith. As the team scrambles for leads, Ronon undergoes a torturous ordeal.

A drive malfunction aboard a mysterious duplicate Daedalus sends the team jumping through various alternate realities where they encounter sinister alien life forms, a searing sun, and a pitched space battle over Atlantis.

A mysterious entity causes crippling havoc within the city's computer systems.

While on a rescue mission to another planet, Dr. Rodney McKay falls fatally ill and his sister Jeannie is summoned from Earth to say her final goodbyes.

While exploring an abandoned catacomb on an unexplored planet, an Atlantis away team uncovers one of Michael's secret labs.

Teyla risks her life on a daring mission aboard a wraith hive ship.

With Hunter Wraith in close pursuit, only Ronan's uncommon skills as a former Runner may save a kidnapped Dr. Keller.

Atlantis encounters a mysterious alien race when Dr. Rodney McKay and a visiting Dr. Daniel Jackson stumble upon the secret lab of a rebellious Ancient scientist named Janus.

With the Daedalus under siege, Dr. Daniel Jackson and Rodney McKay try to keep a reactivated Ancient weapon from triggering a cataclysmic chain of events.

Col. John Sheppard and his team, aided by Dr. Carson Beckett, struggle to save survivors of the Hoffan plague from being sacrificed to the Wraith.

Sheppard and his team are abducted by a newly formed galactic coalition and made to stand trial for crimes against humanity.

An old foe, bent on revenge, infiltrates the Gate Room to take control of Atlantis.

While Richard Woolsey struggles to keep his position as the leader of Atlantis, and McKay and Zelenka investigate a mysterious find, Sheppard is captured by an old enemy with plans to invade the city.

Dr. Keller accompanies Dr. McKay to Earth to attend a top secret scientific demonstration by McKay's former rival.

Atlantis receives a distress signal from a hive ship and discovers that all the Wraith on board have placed themselves in stasis, the victims of a lethal affliction.

Dr. Jennifer Keller wakes to find her consciousness inside the body of a notorious thief who has been sentenced to death for her crimes.

Detective John Sheppard attempts to solve a string of unusual murders in Las Vegas.

Atlantis rushes to destroy an advanced Wraith hive ship before it presents a threat to Earth.

When Rodney McKay realizes Atlantis has started shutting down artificial gravity and collapsing protective shields to compensate for a damaged power system, he turns off all non-essential systems. But when the problem persists, McKay is forced to collapse the shield to the point where it is only protecting Atlantis' main tower, leaving the rest of the city exposed to space.

Lt. Col. Sheppard leads his team to the core of the Replicator home world on a high-risk mission to steal a ZPM, while Col. Samantha Carter, aboard the Apollo, races against time to locate the missing city of Atlantis.

Ronon reconnects with a group of Satedans from his past who enlist the Atlantis team's help on a dangerous mission against the Wraith.

During an exploratory walk on a jungle planet, Lt. Col. Sheppard touches a glowing crystalline growth and unwittingly becomes host to an infectious energy form.

On his way back to Atlantis, Lt. Col. Sheppard and his jumper are taken prisoner by a rogue ship helmed by a beautiful but ruthless human commander with a secret agenda.

With almost everyone on Atlantis infected by an amnesia-causing virus, McKay finds himself zip-tied to his desk with cryptic letters on his arm and no memories of who he is or what has happened.

Arriving on New Athos for an overnight visit, Teyla and Dr. Keller discover the entire settlement abandoned and their own lives in jeopardy from a primitive warrior tribe.

While trying to find her people, Teyla and the team meet a man with extraordinary prophetic abilities who predicts a frightening future for Atlantis.

When McKay's sister Jeanie is kidnapped, the team returns to Earth to find her.

The Atlantis team's worst fears may be realized when a mysterious drone crashes into the city.

Now armed with the means to track Replicator ships throughout the Pegasus Galaxy, the Atlantis teams strives to eliminate the Replicators once and for all.

The Atlantis team successfully salvage a partially damaged Hive ship and in the process retrieve some critical information that may help in their war against the Wraith.

When an alarm sounds throughout the city, initiating a quarantine lock down, the Atlantis team finds themselves trapped in various sections of the city with no way out.

Wanting to maintain diplomatic relations, Sheppard and McKay agree to accompany a precocious young princess on a rite of passage.

When Lt. Colonel John Sheppard receives word that his father has passed away he returns to Earth but, once there, becomes embroiled in a covert and dangerous experiment gone awry.

During an off world mission, Carter, McKay and Dr. Keller become trapped in an underground mining chamber rocked by fierce seismic tremors.

Mr. Coolidge is the newest member of the IOA and openly distrustful of alien participation in any facet of the Stargate program. Despite his bias, the IOA has entrusted him with interviewing Teyla Emmagan and Ronon Dex about their suitability to continue as members of the Atlantis expedition. This does not bode well for Ronon who is next on the list to travel to Earth for questioning.

As Teyla continues to search for her people, a mysterious new illness sweeps throughout the galaxy, killing scores of people.

An old friend's unforeseen return spurs a race against time to rescue a missing teammate.

Following another unsuccessful search for Teyla, Lt. Colonel Sheppard returns home to Atlantis to find the city completely abandoned.

After their temporary alliance with the Wraith backfires, the Atlantis team must find a way to stop two Wraith hive ships that are headed for Earth. Weir orders Colonel Caldwell to attack the Hive ships using the Daedalus and the Orion before she is ordered to return to Earth to account for her team's failures.

Having successfully used the Wraith retrovirus to turn an entire hive ship of Wraith into humans, the team returns to Atlantis with their prisoners in stasis. Weir continues to defend her leadership in the face of an independent review being conducted by IOA member Richard Woolsey.

While looking for suitable stargates to harvest for their new Intergalactic Bridge, the team comes across a small village with a revered leader. To their surprise the village's leader, Lucius, has an obnoxious manner and an utter lack of credibility.

Exploring a village, the team is suddenly attacked and taken prisoner. It turns out that Ronon had visited the planet before, and unknowingly lured the Wraith there. The Wraith then made a pact with the villagers that if they capture Ronon and contact them, the village will be spared from any future culling.

Scouring the Atlantian database Dr. Rodney McKay discovers a reference to an abandoned Ancient testing site. Investigating the site, the team discovers a vast metropolis supporting millions of Ancients. Eager to create an alliance with such an advanced society, Weir is shocked when their leader Oberoth refuses the offer.

Waking up in a psychiatric hospital outside of Washington D.C., Dr. Elizabeth Weir is shocked to discover that her entire experience in Atlantis over the last two years was solely a figment of her imagination. Through the help of her psychiatrist Dr. Fletcher, she learns that a car accident that killed her fiancé left her in a near catatonic state and suffering from delusional psychosis.

Summoned to a planet by a communication code they had previously given their Genii allies, the team is ambushed by Kolya, who has now created his own faction of Genii after being forced from the inner circle of the Genii leadership. While the rest of the team manages to escape, Sheppard is taken prisoner.

Rodney McKay is called back to earth to convince his estranged sister, Jeannie Miller, to assist the Air Force in implementing an important mathematical proof that has application to one of McKay's experiments. Having not seen her in four years, McKay finds it difficult to pry Jeannie away from her family, so he has no choice but to disclose the existence of the Stargate program to her. McKay and Jeannie travel to Atlantis, and begin the experiment, which is intended to generate limitless energy by bridging parallel universes.

Major Leonard's team fails to check in with Atlantis while on a mission exploring an anomalous energy spike. Because the anomaly also makes radio transmission impossible Sheppard must assemble a team in search of the missing men. When the team arrives on the planet they're shocked to find the bodies of several Genii soldiers who have apparently killed each other.

While testing the new McKay-Carter intergalactic gate bridge, the Daedalus detects an Ancient Atlantian warship, traveling at just below light speed and heading towards Earth. Damaged in battle during the war with the Wraith, the Ancients aboard this ship fled the Pegasus galaxy and have spent thousands of years in stasis. Back on Atlantis, the now awoken Ancients meet with General O'Neill and Richard Woolsey. They thank the Stargate team for taking care of the city in their absence, but ask them to vacate Atlantis immediately.

General O'Neill and Richard Woolsey, the lone survivors of the replicators' bloody coup of Atlantis, hide out in an abandoned section of the city. Knowing O'Neil gave General Landry a standing order to nuke Atlantis if a foothold situation should ever arise, the two lay low awaiting their fate.

Teyla begins to see apparitions of ancients in distress and believes they are the ghosts of the Ancients recently massacred by the Replicators. Meanwhile Rodney McKay believes he's found the whale that saved him a year ago while trapped in a submerged puddle jumper. But while taking a jumper out with Col. John Sheppard to investigate his old friend they discover the whale is not alone but is one of dozens of its kind, all headed directly to Atlantis.

Sheppard and his team hear of a great warrior with stories of defeating both the Genii and the wraith and decide to seek him out in hopes of making a powerful new ally. But when they learn this great warrior is none other than Lucius they believe he's up to his old tricks again. Testing him for his enamor-inducing herb they find he's clean and only really guilty of pawning off their battle stories as his own.

Trying to preserve power by turning off all the non-essential systems the Ancients recently activated before being killed by the replicators, Rodney McKay mistakenly is hit by an energy beam from a mysterious device. His worst fears are quickly laid to rest when Dr. Beckett gives him a clean bill of health and returns him to active duty. Not long after the incident Rodney begins to display advanced powers such as amplified senses and telekinesis.

Major Lorne discovers a planet with dozens of satellites in geosynchronous orbit. However, inhabitants on this planet are no further advanced than being themselves in a renaissance period and even stranger, he discovers a flag bearing Rodney McKay's likeness. Informing Rodney and Lt. Col. Sheppard of this, the team realize a game they had found years earlier on Atlantis might actually be much more than just a game.

Investigating what appears to be an abandoned space station inside a hollowed out moon Rodney McKay mistakenly brings one of it's scientists out of stasis. The scientist Henrick explains to the team that the base was the last effort by his people to avoid the repeated culling they've endured for generations at the hands of the Wraith. Using the Wraith stasis technology they modified a chamber to hold a large number of their people for thousands of years in the hope the wraith would find their empty planet and believe they had disappeared.

With the entire city ordered to take a personal day the team does their best to unwind and enjoy their leisure time. Without warning a mysterious explosion rips through the city killing and injuring unsuspecting citizens. Dr. Rodney McKay and Dr. Carson Beckett arrive on the scene to find Teyla critically injured by shrapnel from the explosion. Unable to find explosive residue, the only leads they have to go on are eyewitness accounts saying one of the base-scientists just suddenly exploded.

Deep underwater, the team scours the ocean floor looking for a mobile geothermal drilling station the ancients left dormant in hopes of unleashing near limitless power from beneath the planet's surface. The team finds the drilling rig and cautiously explores the station the Ancients chose to abandon.

After helping relocate the Taranans, the Atlantis team realizes they haven't heard from the village in an unusually long period of time. Wondering what happened to them, Weir sends Sheppard and his team to go investigate their village. Once there, it appears the Taranans have just abandoned their village until Rodney McKay detects life signs well beneath the surface in the remnants of the previous village's underground industrial complex.

With the arrival of the Apollo to Atlantis comes intel that the Replicators appear to be building a large armada to directly attack earth. Planning to strike first, Col. Ellis with the aid of the Atlantis team launches a surgical strike nuking the entire armada. Believing that all imminent danger has been avoided the team is shocked when a satellite housing a stargate takes up geosynchronous orbit above Atlantis.

Rescued from a near-fatal encounter with the Wraith, Lt. Aiden Ford receives medical care at the Atlantis base. However, his abnormally quick recovery leads Dr. Beckett to worry that the Wraith who attacked Ford may have injected him with a harmful enzyme, causing long-term and unpredictable damage. Meanwhile, as the Wraith's siege of Atlantis rages on, Sheppard finds himself surrounded by the enemy. He is rescued by the timely arrival of Colonel Steven Caldwell, commander of the Daedalus. Launched from Earth and sent in to assist the Atlantis team during battle, the Daedalus helps to defeat the Wraith's first wave assault on the city. Their relief is short-lived, however. The team soon learns that the Wraith are planning the next wave of their onslaught -- an entire fleet is about to descend on the city. With a little over a day before the assault, Dr. Weir realizes that the Daedalus will not be enough to fight the Wraith's forces. McKay devises a drastic plan – but there may not be enough time to perfect the complicated technology his plan requires before the Wraith arrive.

When a scientist is killed in the Daedalus' computer room, McKay first believes the poor circuitry is at fault. However, when another scientist is killed while investigating the death, McKay begins to suspect that someone – or something – is deliberately planning these breakdowns. Soon after, McKay is alerted to a virus on one of the ship's computers. When he runs its code through a translator, he is shocked to discover that it is written in Wraith. Even worse, he learns that the virus has the ability to re-write itself, making it seemingly impossible to conquer. Realizing that the program's capability to mutate has virtually given it a mind of its own, McKay worries that the Wraith may use the virus to take control of the ship – with potentially deadly results. As feared, the virus' artificial intelligence soon takes control of the Daedalus' auxiliary ships, and the crew becomes increasingly powerless to defend themselves. Fearing that the Wraith will use the Daedalus' advanced features to attack Atlantis, McKay and Sheppard race against the clock to counteract the virus before the Wraith turn the Daedalus' advanced technology against the city.

When a routine, off-world science mission comes across a mutilated Wraith carcass, the team suspects Ford may be involved. Intrigued, they split into teams to investigate. Teyla and Sheppard encounter Ronon Dex, a fierce warrior who survived a battle with a Wraith seven years earlier and has been on the run ever since. When Dex reveals to Teyla and Sheppard that Ford has taken up residence on the planet, they enlist his help to locate their friend. The duo hope to rehabilitate Ford to his former state. McKay eventually stumbles upon the increasingly incoherent and maniacal Ford, and tries to reason with his former colleague and friend. However, McKay begins to see how far gone Ford has become -- addicted to the enzyme injected in him by the Wraith who attacked him, Ford has been brutally killing Wraith to get a fix of the solvent. Reluctantly, McKay and the rest of the crew must face the realization that they may never be able to save Ford from what he has become.

During an investigation of a planet leveled by a Wraith attack, McKay and new security team member Lt. Laura Cadman are transported aboard a Wraith Dart, which subsequently crashes. Unfamiliar with the Wraith technology, Atlantis scientist Dr. Zelenka is only able to transport McKay out of the rubble. Cadman's body is nowhere to be found. Zelenka believes that she is still trapped inside the Dart, until McKay claims to hear her voice – coming from inside his own head! It seems that Zelenka's experiment, rather than saving the two separately, caused them to unite – and Cadman must remain inside of McKay's head until Zelenka can figure out a way to separate the pair. Meanwhile, as Ronon Dex settles in at Atlantis, he shows off his impeccable fighting skills during arsenal training. Impressed, Sheppard implores Weir to put aside her reservations about the newcomer and consider allowing Ronan to join the Stargate Atlantis team.

When the Atlantis team sets out to a distant planet, they land on a small island off the main coast and are attacked by a group of savages. Barely escaping the island with their lives, the team is rescued by one of the planet's security vessels and brought to the considerably more civilized mainland. Once safely on shore, the team learns that the island had been set aside for the banishment of prisoners and is susceptible to Wraith attacks. The rest of the planet, however, is immune to such Wraith assaults. Intrigued by this, as well as by the planet's unconventional energy source, the team tells Weir of their discovery. However, when Weir arrives on the planet to investigate further, she begins to suspect that the mainland's idyllic environment may be the result of a sinister pact between the planet's leader and the Wraith.

While doing standard recon on a planet thought to have been destroyed by the Wraith long ago, the team finds an Ancient structure standing intact amidst the ruins. After some investigating, they discover that the monolith served as a military research facility where the Ancients worked to develop an advanced method of harnessing energy. When the Wraith attacked before the project could be completed, the underdeveloped technology malfunctioned and destroyed the civilization. McKay theorizes that if the powerful technology is fully developed, it could serve as a potent source of energy for Atlantis. Hope turns to fear, however, when McKay's first attempt at reviving the energy source results in the death of one of the Atlantis scientists. Despite the team's apprehension, a determined McKay insists on moving forward with finishing the project. But can McKay unravel the intricacies of the Ancients' technology without putting himself and Sheppard in mortal danger?

On an unexplored planet, Sheppard, McKay, Teyla and Ronon hike into a village at dusk. The startled inhabitants insist that they spend the night. Apparently, after darkness falls, a mysterious killer stalks the area, sucking the life from its victims. Sheppard and his team instantly guess what they're dealing with: a Wraith.

Having been savagely bitten by the Wraith girl Ellia, Sheppard hurries back to Atlantis for medical treatment. Both he and Dr. Beckett are shocked, however, when they realize that the wound has vanished. Sheppard's arm is completely free of any trace of the bite.

When Atlantis's deep-space sensors detect the Aurora, an ancient Atlantian warship, at the edge of the galaxy, Sheppard's team wastes no time hitching a ride to it aboard the Daedalus. Upon their arrival, they encounter a Wraith scout ship. They destroy the scout before it can cause trouble — or so they hope.

While exploring a new planet, Sheppard, McKay, Teyla and Ronon are ambushed by a group of men armed with Wraith stunners. They awaken to find themselves prisoners in a cave, where they discover the mastermind behind the attack: Lt. Aiden Ford.

Colonel Sheppard and his team find themselves prisoners of the Wraith following Ford's attack on a hive ship. Dr. McKay goes to great lengths to help them.

On a new planet, Sheppard, McKay, Teyla, and Ronon discover an intriguing portal in a mountainside: an opaque force field surrounded by Ancient text. After inserting a camera through the field to check for danger, Sheppard decides to enter the portal himself. The instant he begins, however, he feels terrible pain. His teammates struggle to pull him back out, but the portal inexorably sucks him through.

On Earth, a galaxy away from Atlantis, Gen. Landry receives intelligence that The Trust, a group of conspirators controlled by the evil Goa'uld, have learned of the Ancient city and sent an undercover operative there to plant a bomb. Details are sketchy, but any use of Atlantis's stargate to dial Earth will somehow trigger the explosion.

During the first test flight of a Puddle Jumper that Dr. Zelenka has repaired, the small ship abruptly crashes and sinks into Atlantis's ocean with Dr. McKay and the pilot, Griffin, on board.

Sheppard, McKay, Teyla and Ronon visit an oppressed, poverty-stricken village that sacrifices half of every harvest to a mysterious Lord Protector in a great tower — a tower that looks exactly like the central spire of Atlantis. In exchange for the farmers' tribute, the Lord Protector defends them from the Wraith with amazing weaponry.

Above an isolated moon, Sheppard's team discovers two battered life pods in decaying orbits. They bring them to Atlantis, where Dr. McKay opens the first pod. An aged, unconscious woman lies within, near death. When Dr. Weir approaches for a closer look, an energy beam lances out of the pod and strikes her. Weir collapses.

Col. Sheppard's team is urgently summoned to M1K-177, where Maj. Lorne's team has been attacked. When Sheppard and his unit arrive, however, all they find is a burned building containing charred bodies: presumably, Lorne and his men. After returning to Atlantis, Sheppard and Weir are startled when Ladon Radim, a member of the Genii strike force that previously tried to attack the city, contacts them through the stargate. He claims that he wants to trade a ZPM in exchange for weapons to stage a military coup against Cowen, the ambitious Genii leader.

Lt. Michael Kenmore awakens in Atlantis's infirmary with no memory of how he got there — or who he is. Dr. Weir, Col. Sheppard and Dr. Beckett explain that he's a member of the expedition's military contingent who was captured by the Wraith during a dangerous mission. Although Sheppard's team rescued him, he was badly injured and has been unconscious for days.

Sheppard's team visits the planet Taranis at the invitation of two leading citizens, Dr. Norina Pero and Chancellor Lycus, who want McKay to repair a failing shield generator at an Ancient base they've discovered. Lycus also shows the team a massive Ancient warship, much like the Aurora, hidden in a vast warren of tunnels beneath the base. Although the warship is damaged and currently inoperable, Dr. Weir eagerly opens trade negotiations with Lycus as soon as she learns of its existence.

A Wraith hive ship arrives in orbit above Atlantis. In the cloaked city below, everyone is stunned when Michael radios down with an unnerving request: He wants to negotiate an alliance.

The Stargate SG-1 team discovers what they believe to be the remnants of the lost city of the Ancients – the originators of the Stargates and Stargate Command launches an investigation to find the mythical city of Atlantis. Situated in the distant Pegasus Galaxy, it's farther than any Stargate team has ever traveled. With only enough power to make a one-way trip, a new team, headed by civilian Dr. Elizabeth Weir, is formed and travels through the gate to this unknown galaxy. There, they discover the marvels of the lost city of Atlantis…. and encounter a sinister new enemy.

The Stargate SG-1 team discovers what they believe to be the remnants of the lost city of the Ancients – the originators of the Stargates and Stargate Command launches an investigation to find the mythical city of Atlantis. Situated in the distant Pegasus Galaxy, it's farther than any Stargate team has ever traveled. With only enough power to make a one-way trip, a new team, headed by civilian Dr. Elizabeth Weir, is formed and travels through the gate to this unknown galaxy. There, they discover the marvels of the lost city of Atlantis.... and encounter a sinister new enemy.

Dr. Rodney McKay undergoes experimental gene therapy, altering his DNA to match the Ancient genetic coding. The experiment opens up countless scientific possibilities, as well as an unexpected problem. Meanwhile, during a game of hide and seek, one of the Athosian children inadvertently opens a containment unit that lets loose a seemingly harmless black ethereal cloud. But when Atlantis goes through a series of technical malfunctions, they realize that the shadowy creature is actually feeding off of the power supply!

Fleeing from a surprise encounter with the Wraith, Major Sheppard falls victim to an alien symbiote which is feeding off his life force and slowly paralyzing him. While speeding back to Atlantis for medical aid, the team gets trapped halfway through the Stargate when the puddle jumper, damaged in the altercation with the Wraith, suffers a mechanical failure. With only thirty-eight minutes before the Stargate shuts down, Lieutenant Ford and Dr. McKay struggle to manually fix the problem. As the clock ticks away, the Atlantis team must come together, or perish in the harsh vacuum of space.

When the Atlantis team is ambushed by the Wraith on a trip off-world, Dr. Weir begins to suspect that one of the Athosians is actually a Wraith spy. Gate travel is suspended until both parties are separated to different areas of Atlantis. But on their first mission back through the gate, Teyla disappears and the Atlantis team is once again ambushed by the Wraith. With the Athosians secured away from the gate, suspicions rise and tensions increase…could Teyla have been the traitor in their midst all along?

During an exploratory mission, the puddle jumper's electrical systems are knocked out by a massive electromagnetic field and the team is forced to make an emergency landing. They soon encounter a primitive tribe of children who have been untouched by the Wraith for centuries due to the protective force of the electromagnetic field. But the children believe it is their ritual of mandatory suicide at the age of 25 that keeps the enemy at bay, despite the contrary insistence of the Atlantis team. Fearing the "full growns" in their midst will attract the Wraith, the villagers become anxious for their unexpected guests to leave as soon as possible. But to be able to leave, Dr. McKay must first disable the electromagnetic field. In doing so, he unwittingly trips a Wraith silent alarm, leaving the tribe open to attack.

The Atlantis team encounters the Hoffans, a human civilization in the process of rebuilding their society since the last attack of the Wraith. The resilient Hoffans have developed the beginnings of a drug that could potentially make them immune to their enemies. Fearing that the next Wraith culling will come before they are able to complete their tests, the leaders demand that their people be inoculated before the drug can be proven safe. Dr. Beckett argues that there is no way to know what the true effects of the drug will be. Can Beckett make the Hoffans see reason, or has their haste made them blind to the epidemic they may be unleashing upon themselves?

With the city's food supply dwindling, the Stargate Atlantis team must search for an alternate food source. At the suggestion of Teyla, they meet with Cowen, the leader of a simple group of farmers known as the Genii. Untrusting of outsiders, Cowen is hesitant to agree to any sort of trading. However, he soon changes his tune when Major Sheppard demonstrates the Atlantis team's advanced weaponry, including C-4. His interest piqued, Cowen agrees to supply the Atlantis team with food in exchange for the explosives. Elated, Sheppard and Dr. McKay return to Atlantis to report their success to Dr. Weir, while Teyla and Lieutenant Ford enjoy the Genii's Harvest Ceremony.However, when Sheppard and Mckay return to the Genii village, they stumble upon technology that leads them to believe the Genii are not at all what they seem.

During an exploration of a planet with no apparent inhabitants, Dr. McKay discovers that the planet's fog-like atmosphere is actually pure energy… enough to open a wormhole back to earth. Wanting to be sure they could return to Atlantis to continue their mission, Dr. Weir relays a message back to Stargate Command. They are told that the battleship Prometheus has been outfitted with a hyperdrive and they would be able to return to Atlantis within a month! Back on Earth, the team is overjoyed to be with the things and people they love. However, when the Prometheus' hyperdrive is accidentally destroyed, their hopes of ever returning to Atlantis are suddenly dashed.

The team learns that a storm of catastrophic proportions is headed straight for the city of Atlantis. Without enough energy to power the shields, Dr. Weir orders that Atlantis be evacuated until the storm passes. But Dr. McKay conceives of a last minute plan to save the city – harness the power of the electrical storm to fuel the shields. Meanwhile, unbeknownst to the Atlantis team, the Genii have learned of Atlantis' evacuation, and devise a dangerous plan to take over the city's weapons for themselves. With Weir and McKay taken hostage and Lt. Ford and Teyla aiding the evacuees, it is up to Major Sheppard to shut down the remaining grounding stations and save Atlantis from invasion before the storm hits.

When an approaching storm with awesome destructive capabilities causes Dr. Weir to evacuate the city, the Genii launch an invasion, and take control of Atlantis' weapons. With Dr. Weir and Dr. McKay taken hostage and Major Sheppard fending for himself against the ruthless Genii troops, the rest of the Atlantis team desperately tries to find a way to get back to the city while the storm rages around them.

Leading an exploration of an ancient weapons satellite in deep space, Major Sheppard and Dr. McKay intercept a Wraith distress signal. Deciding to investigate, the team lands on a nearby planet and finds the source of the call - a downed Wraith cargo ship. When the unseen Wraith awakens from hibernation, Sheppard and McKay become the focus of its ravenous appetite.

While assessing the structural damage to the city caused by a massive storm, two of Dr. McKay's team of scientists experience horrifying visions. Minutes later, they drop dead. Retracing the steps of the dead scientists, McKay and his team find an Ancient lab, its contents in disarray. Afraid of a viral outbreak, Dr. Weir places the city under a self-regulated quarantine. Even with the city under lockdown under the threat of a possible viral outbreak, more and more people begin suffering from the same terrifying visions. If McKay cannot find a cure, the entire city will be doomed.

Engaged in combat, the Atlantis team's puddle jumper is hit with an energy wave that leaves them unharmed, but destroys their Wraith attackers. Hoping to find the source of the wave, the team lands on the planet below. There they find a civilization enjoying the utmost health and happiness, untouched by the Wraith. Their leader, Chaya, refuses to allow anyone other than her own people the sanctuary and safety from the Wraith that would be found by settling on their planet. Unwilling to give up so easily, Major Sheppard asks Chaya to reconsider. After thinking it over, Chaya surprises everyone by requesting to accompany them back to Atlantis to discuss the matter further leading the team to suspect they may be caught in a trap.

While exploring the city, the Atlantis team discovers a stasis chamber holding a woman who appears to be over 10,000 years old. Excited at the possibility that she is one of the Ancients, the alien race that built Atlantis, the team decides to bring her out of stasis despite the risk to her health. Everyone is shocked when, once re-animated, the elderly woman identifies herself as none other than Dr. Weir.

The Atlantis team travels to Dagan, a planet with a hidden ZPM and a mysterious trail that will lead to its hidden secret chamber location. But the Genii have learned of the Atlantis team's activities on Dagan. Realizing the ZPM must hold awesome power, the Genii plant a sleeper agent amongst the Daganians aiding the Atlantis team on their search. Now, as the Atlantis team closes in on the location of the ZPM, the Genii close in on them.

Having learned that the entire Wraith armada is headed towards the city, the Atlantis team prepares to send a data message to Earth with information about the Wraith threat, and what could be their last messages home to loved ones.As the rest of the team records their touching and often humourous messages back home, Major Sheppard and Teyla embark on a reconnaissance mission where they witness the vastness of the Wraith army, and look on helplessly as the Wraith cull the planet's helpless inhabitants.

Terrifying nightmares about the Wraith cause Teyla to lash out at her colleagues and prompt her to seek professional advice. With psychological guidance, she discovers that she can sense the Wraith. In their search to learn more, Teyla and the Atlantis team discover important information that may hold the key to understanding their enemy, including the disturbing possibility that Teyla's connection to the Wraith could be the result of genetic experimentation.

With the Wraith armada closing in on Atlantis, Dr. McKay and a small team attempt to repair an ancient weapons satellite in the hopes of leveling the odds in the coming battle. Meanwhile, tension builds between Teyla and some of the other members of the Atlantis team over her connection to the Wraith. Major Sheppard steps in to defend her, but even he begins to harbour doubts when a team member is left unconscious after an attack by an unknown assailant.

With the Wraith armada bearing down on the city, the Atlantis team prepares to evacuate. Setting the city's self-destruct sequence, they hope to make it impossible for the Wraith to gain access to Earth. Things begin to look up when reinforcements from Earth are brought in and it is announced that the battleship Daedalus will arrive in four days. However when the warheads are easily destroyed by the Wraith, and the first wave of Wraith attackers strafe the city with weapons fire, it becomes increasingly clear that the added reinforcements are not going to be enough. With time running out, the Atlantis team must turn to the least likely source of aid - the duplicitous Genii! But with the Wraith overrunning the city, even the Genii's help may not be enough.