Stargate Atlantis

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.