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- TV Show Ended -
There is no Next Episode of Stargate Atlantis planned.
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. Zalenka is only able to transport McKay out of the rubble. Cadman's body is nowhere to be found. Zalenka 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 Zalenka's experiment, rather than saving the two separately, caused them to unite – and Cadman must remain inside of McKay's head until Zalenka 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.