Colonel Abe Ellis arrives at Atlantis with a new Earth ship, The Apollo and a new mission. Dr. Weir has misgivings about that mission, one that could start a war with a very powerful enemy. When his mission goes wrong, Weir must take radical action to save Atlantis.
With a group of Wraith Hive ships on the way to Atlantis, the team searches for a place to flee and a way to destroy the city. McKay leads a team to try and activate the Ancients' orbital weapons platform.
While shutting down unnecessary systems in Atlantis, McKay is zapped by a strange Ancient machine. He begins to have superpowers, but things are never as they seem, and Rodney and the team must race against his mutations to save his life.
Major General Jack O'Neill's mission to defend Atlantis fails as he and Richard Woolsey are taken prisoner during a Replicator assault on the city. Sheppard's team, Dr. Weir and Dr. Carson steal a Jumper from Stargate Command on Earth and come back to Pegasus galaxy with a plan to retake Atlantis.moreless
Earth's new battlecruiser Daedalus arrives under the command of Colonel Caldwell and saves Major Sheppard from his suicide run on the Wraith Hive ships. McKay and his team must get the new ZPM installed and raise the city shields to protect Atlantis before the rest of the Wraith fleet arrive to take the city.moreless
Two Wraith Hive ships have captured Dr. McKay and Ronon and are on their way to Earth. It is up to Colonel Sheppard to rescue them and figure out a way to stop the Wraith from reaching a "new feeding ground".
While testing a chain of Stargates that will allow travel from Atlantis to Earth in about 30 minutes (the "McKay-Carter Intergalactic Gate Bridge"), McKay, Sheppard and the team discover an Ancient ship traveling at almost the speed of light.
When Dr. Weir talks to the travelers, she is surprised by their request that the expedition members vacate the city of Atlantis.moreless
The discovery of an outpost, left behind by the Ancients in the most unlikely of places, leads a new Stargate team to the distant Pegasus galaxy. Once there, they discover a planet of humans being decimated by a terrible alien race know as the Wraith.
Todd informs Atlantis that a rogue Wraith has acquired several Z.P.M.'s to power a formidable new Hive ship. When the Daedalus engages it in battle but is unable to defeat it, the team gets a message indicating it is headed to Earth.
Sheppard returns from a mission and finds Atlantis abandoned and surrounded by sand dunes. He soon finds a hologram of Dr. McKay, who tells him he has come 48,000 years into the future, and everyone is long dead. But the McKay hologram has a plan to save the city and restore Sheppard to his own time.moreless
When his sister Jeannie comes up with a vital mathematical proof, Rodney returns to Earth to take her back with him to Atlantis. But things become complicated when another Rodney McKay from a parallel universe arrives.
While a disease spreads through the Pegasus Galaxy, Teyla believes the father of her child is trying to communicate with her. While searching for answers, the team comes across a very interesting discovery.
The inhabitants of the city and the mainland are forced to evacuate when a huge hurricane bears down on them. But things get even worse when the city is then captured by the Genii, forcing Sheppard to try and stay one step ahead when they capture Weir and McKay.
To while away the hours, Sheppard and McKay have been secretly competing against one another in a real-time strategy game they discovered on Atlantis. To their surprise, they discover that this is more than just a game....
The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis' future. Meanwhile, they join forces with a Wraith in an attempt to fix the virus Rodney created earlier to stop the Replicators, that has since malfunctioned. Woolsey arrives at Atlantis to conduct an evaluation of Carter's command.moreless
While exploring the mainland of Atlantis' planet, Sheppard is captured by a foe believed to be long dead. Meanwhile, Woolsey's job is at risk and he has an important decision to make and McKay and Zelenka make an interesting undersea discovery.
When a deadly infection causes key members of Atlantis to lose their memories, it's up to Teyla and Ronon to find a cure. But when the Marines begin hunting down everyone and no one remembers why, it's hard to work together to cure everyone.
The Puddle Jumper has been damaged and is stuck part way through an Orbital Space Gate. The team have only 38 minutes to find a way to dislodge themselves before the Stargate shuts down, cutting the Jumper in half. To make matters worse, John Sheppard has an alien creature attached to his neck that is sucking the life from him.moreless
Gating to the planet Genii to trade for food, the team discovers what appears to be a simple, farming population. But they are preparing a deadly weapon to attack the Wraith, and when Sheppard and McKay are interrogated it appears the Genii may not make the best of allies.
Sheppard's team discovers a planet untouched by the Wraith because the government sends their criminals to a penal island for the Wraith to feed upon. Sheppard's Jumper is shot down and crashes on the island.
Daedalus is infected by a Wraith computer virus. Dr McKay and his team must stop it as members of the Atlantis expedition return from Earth after a meeting at the SGC thanks to the ZPM. During the meeting at the SGC, Dr. Weir learns that the Pentagon plans to replace Major Sheppard with Colonel Caldwell.moreless
Ronon Dex discovers that a small number of his people survived the Wraith attack on his planet, including his former military trainer, with whom he has unfinished business. Meanwhile, McKay puts Atlantis at risk when he tries to unlock the secrets of an Ancient power source.
With a brief opportunity to send a data transmission to Earth, members of the Atlantis expedition compose video messages home to their loved ones. Meanwhile, Sheppard and Teyla use the Stargate to take a Jumper to do some reconnaissance on the approaching Wraith fleet.
The planet Dagan may be home to a vitally important ZPM, capable of restoring Atlantis' shield and protecting the city from the Wraith, but a mysterious 'Brotherhood' on the planet - and their knowledge of the Genii - suggest that the planet may not be what it seems.
The Atlantis team encounters a pre-technological world strangely untouched by the Wraith. They hope to negotiate with the local population to provide a home for the refugees of Wraith attacks, currently living in Atlantis.
The Atlantis team uncovers the last survivors of a civilization who have been placed in suspended animation aboard a space station. As some of the people awaken, problems from the past threaten to destroy everyone on the station, including Sheppard.
Colonel Sheppard is separated from his team while investigating an Ancient device; he finds himself in a domain where time is dilated, progressing faster than normal. Doctor McKay frantically looks for a way to save Sheppard before time runs out!
The team discovers an exact replica of Atlantis on a planet they are exploring. The planet is protected by The Protector who uses the technology to keep the villagers in line and the Wraith away. The Protector is dying and Sheppard is caught up in a dispute among the heirs of the throne.moreless
During a mission, Sheppard and his team learn that a lone Wraith -- whose dart had crashed leaving him unable to get to the spacegate -- has been terrorizing a village for some ten years. They offer to help, but soon after they begin to hunt, Teyla senses that something is different about this Wraith.moreless
When the Wraith discover that a small group of survivors of Michael's release of the modified Hoffan drug are hiding among the population of a village on another planet, Sheppard and his team must convince the entire village to evacuate before a Hive Ship arrives.
When Sheppard and his team are about to return from an off world mission with their Puddle Jumper, the systems of the Jumper go crazy. Barely able to return to Atlantis, the Jumper seems to infect the city's systems with what seems to be a computer virus.
Colonel Carter joins Dr. McKay and Dr. Keller on an off-world mission, to convince the people of a world rocked by earthquakes, to relocate. However, things take a turn for the worst when they are plunged into a sinkhole and become trapped in an old Genii mining facility.
A thief uses an Ancient transfer device to switch her consciousness with Dr. Keller. While she attempts to escape Atlantis, Dr. Keller must deal with the thief's accomplices and angry villagers on her trail.
When Sheppard and his team are brought to trial by a Coalition of human worlds for what they claim are crimes against the people of the galaxy, it's up to Woolsey's legal expertise to clear their names.
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