A woman is found in suspended animation in Atlantis, and the team is shocked to see that it is Dr. Weir herself, who tells them of her trip 10,000 years into the city's past.

The team discovers a young Wraith girl who has been raised by a human, and is in hiding from the people of her human village in fear of her life.

When an operative of the Trust plants a bomb in Atlantis, the team must find a spy within their own ranks before the Wraith arrive and discover the city.

The team finds a world that possesses Ancient defense technology, where Colonel Sheppard finds himself a pawn in the rivalry between the heirs to the throne.

The team discovers two pods that contain the minds of alien beings, who take control of Weir and Sheppard's bodies to continue their personal war.

Michael and his Wraith faction arrive at Atlantis to propose an alliance, hoping to use the retrovirus to transform their Wraith enemies into prey.

Weir and the team visit an advanced civilization that split off from the Lanteans thousands of years ago, but discover that they may not have left Atlantis in peace.

The Atlantis team investigates the disappearance of one of their allies, only to find an old enemy engineering a race of powerful monsters.

Colonel Sheppard and his team embark on a risky mission to steal a Z.P.M. power module from the Replicators -- but must rely on a compromised Dr. Weir to succeed.

During a visit to New Athos, Teyla and Dr. Keller find themselves on the run from a primitive tribe of warriors.

The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis's future. The Wraith seek a new alliance with Atlantis in their war with the Replicators.

Rodney McKay goes in search of his sister on Earth after she is kidnapped by the head of a powerful corporation.

With a plan to potentially extinguish the Replicator threat, the Atlantis team must seek an alliance with a fleet of Wraith ships.

An automated lockdown traps Atlantis personnel in various parts of the city, each of them hoping the others will come to their rescue.

While on personal leave on Earth, Sheppard and Ronon learn that scientists have engineered a human-form Replicator -- who is now on the loose.

Teal'c visits Atlantis to counsel a headstrong Ronon, who is up for review by the I.O.A. But the two must work together when the Wraith invade the Midway space station in order to reach Earth.

Lt. Colonel John Sheppard and his team are trapped under the rubble of Michael's facility in order to rescue Teyla Emmagan. As Colonel Samantha Carter launches a team to rescue the rescuers, little do they know that Michael Kenmore is also searching the planet for the survivors.

The Atlantis expedition mysteriously finds the Daedalus, abandoned and drifting in space. When Lt. Colonel John Sheppard's team come to investigate, the ship mysteriously disappears. They soon discover that the ship is actually an alternate Daedalus from a Alternate reality, and the team must find a way back to their Universe or risk being stranded forever in an unfamiliar reality.

Dr. Rodney McKay is infected with the Pegasus equivalent of Alzheimer's disease, known as Second Childhood, a common illness among the elderly in the galaxy. The only way to save him is a shrine on Talus. The downside is that it has turned into a Wraith outpost.

Dr. Daniel Jackson arrives in Atlantis to investigate a hidden lab left behind by the rogue Ancient scientist Janus. Their discovery has attracted the attention of a mysterious group of aliens, who infiltrate the city. Meanwhile, "Todd" and a delegation arrive on the Daedalus to bring forward Dr. Jennifer Keller's gene therapy.

As Dr. Rodney McKay and Dr. Daniel Jackson is held prisoner by the Vanir, they make a startling discovery about who they really are. Meanwhile, "Todd" and his Wraith hijack the Daedalus to find and destroy those who activated the Attero device. The Travelers arrive and Lt. Colonel John Sheppard must help them get to the planet before "Todd" uncovers a way to discover the device for good, even if it means sacrificing McKay and Jackson's lives to do so.

Michael Kenmore has infiltrated Atlantis with an army of his Hybrids, and closes off Stargate Operations and the surrounded levels to prevent anyone from taking it back. His plan; take Teyla Emmagan and her child to perfect his Hybrids, and to destroy the base when they're done. Meanwhile, Lt. Colonel John Sheppard, Dr. Rodney McKay and a team try to take back the city before Michael leaves with what he wants.

After a Wraith Hive Ship shows up over Atlantis transmitting a distress call, Lt. Colonel John Sheppard's team discovers that its crew has been stricken with a disease they helped create.

"Todd" informs the Atlantis expedition that a rogue group of Wraith has acquired several Zero Point Modules to power a Super-hive, and wants it destroyed. However, after the Daedalus is disabled, they learn that the ship is heading straight for Earth, and they must stop it before it gets there.