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The Atlantis base is threatened when the team discovers that an alien entity is in the city. McKay’s experiment with alien technology goes awry.

The S.G.C. is put under quarantine after a mysterious infection leaves a Russian officer in the infirmary — but the disease may not be a disease at all.

New York City firefighter, Tommy Gavin, cannot escape the ghosts of those who have died around him as he faces the everyday challenge of saving lives while trying to fix his own.

Carl Morrissey is a lowly supermarket employee who happens to be one of the 4400 returned abductees. He uses his new found powers – enhanced reflexes and strength – to become a vigilante and fight crime in his neighborhood. Meanwhile, Lily is thrown in jail for violating the restraining order while looking in on her daughter and ex-husband’s new life. After picking up Lily from the police, Richard and Lily go back to the apartment they now share and we see the romance between the two begin to become more serious. Also, Shawn begins to learn more about his healing powers, and we are left with a cliffhanger ending of whether he will heal his cousin.

A new Stargate team embarks on a dangerous mission to a distant galaxy, where they discover a mythical lost city — and a deadly new enemy.

Sheppard tries to convince Weir to mount a rescue mission to free Colonel Sumner, Teyla, and the others captured by the Wraith.

Everyone on Earth is excited about a comet passing by, but as soon as its trajectory changes to a collision course, everyone starts to panic. The comet turns out to be a giant ball of light that, after exploding, leaves behind 4400 people. They are missing persons who have been gone from a few months to 60 years, and none have aged a day. The 4400 are put in quarantine and eventually released. Some of the returnees begin to exhibit strange and uncontrollable new abilities. Tom Baldwin and Diana Skouris, two Homeland Security agents, are appointed to find out what happened to the 4400.

Carter and Teal’c go in search of the Asgard to try and save Colonel O’Neill, but discover that the Asgard’s enemy has returned with a vengeance. The System Lords seek an alliance with Earth against a common enemy.

While the Goa’uld threaten to attack Earth, SG-1 and the Asgard make a last, desperate stand against the Replicators, which have captured Major Carter and invaded the last outpost of the Asgard civilization.

Jack and Chase must make a powerful sacrifice when dealing with the virus.

Tony is able to help Jack one last time before he is taken into custody, while an angry victim seeks vengeance on Saunders.

Palmer makes a surprising career choice in the wake of Sherry’s death.