Stargate Atlantis

After their alliance with the Wraith backfires, the team must find a way to stop two Hive ships that are headed for Earth. Weir orders to attack and Sheppard is forced to rely on Michael to help him save McKay and Ronon, who are being held prisoner.

Successfully using the 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 the IOA.

The team comes across a small village with a revered leader. Beckett soon becomes so enamored by his host he brings him to Atlantis. But soon, McKay discovers that Lucius is using some sort of pheromone to enchant those around him.

Exploring a village, the team is suddenly attacked and taken prisoner as Ronon had unknowingly lured the Wraith there. The villagers set Sheppard and Teyla free, who mobilize a strike force. When they return, the village has been devastated.

Dr. McKay discovers a reference to an abandoned Ancient testing site. At the site, the team discovers a vast metropolis supporting millions of Ancients. Eager to create an alliance, Weir is shocked when their leader Oberoth refuses the offer.

Waking up in a psychiatric hospital outside of D.C., Weir is shocked to discover that her entire experience in Atlantis over the last two years was all in her imagination. She learns that a car accident left her suffering from delusional psychosis.

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

McKay is called back to earth to convince his estranged sister, Jeannie Miller, to assist the Air Force. McKay and Jeannie travel to Atlantis, and begin the experiment which is initially successful, until a McKay from the parallel universe appears.

Major Leonard's team fails to check in with Atlantis while on a mission. Following the energy readings in hope of finding Major Leonard and his men, McKay leads the team into a cave to discover that the cause the energy spike is a Wraith generator.

The now awakened Ancients meet with O'Neill and Woolsey, thanking them for taking care of the city but also asking them to vacate Atlantis. While Ronon and Teyla stay in the Pegasus galaxy, the rest struggle to resume their lives on Earth.

O'Neill and Woolsey, the lone survivors of the replicators' bloody coup, hide out in an abandoned section of the city. Knowing Landry has an 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. McKay believes he's found the whale that saved him a year ago while trapped in a submerged puddle jumper.

The team hear of a great warrior with stories of defeating both the Genii and Wraith and seek him out in hopes of making a new ally. But when they learn this great warrior is none other than Lucius they believe he's up to his old tricks again.

Trying to preserve power by turning off all the non-essential systems the Ancients recently activated before being killed by the replicators, McKay mistakenly is hit by an energy beam from a mysterious device.

Lorne discovers a planet with dozens of satellites in orbit. However inhabitants on this planet are no further advanced than the renaissance and have a flag with McKay's face. The team realize a game they had found earlier might be more than a game.

Investigating an abandoned space station, McKay mistakenly brings one of it's scientists out of stasis. The scientist explains to the team that the base was the last effort by his people to avoid the repeated culling they've endured by the Wraith.

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.

The team searches the ocean for a mobile geothermal drilling station the ancients left dormant. Cautiously exploring the station, Teyla thinks she senses the presence of a Wraith. Weir, believing it's pressure affecting Teyla, has the team press on.

After helping relocate the Taranans, the Atlantis team realizes they haven't heard from the village in a long period of time. It appears the Taranans have just abandoned their village until McKay detects life signs well beneath the surface.

The team is shocked when a satellite housing a stargate takes up orbit above Atlantis. When the stargate begins transmitting an energy beam, attacking the city, McKay takes a page from the Ancients and opts to sink Atlantis back into the ocean.