Following another unsuccessful search for Teyla, Lt. Colonel Sheppard returns home to Atlantis to find the city completely abandoned.

An old friend's unforeseen return spurs a race against time to rescue a missing teammate.

As Teyla continues to search for her people, a mysterious new illness sweeps throughout the galaxy, killing scores of people.

Mr. Coolidge is the newest member of the IOA and openly distrustful of alien participation in any facet of the Stargate program. Despite his bias, the IOA has entrusted him with interviewing Teyla Emmagan and Ronon Dex about their suitability to continue as members of the Atlantis expedition. This does not bode well for Ronon who is next on the list to travel to Earth for questioning.

During an off world mission, Carter, McKay and Dr. Keller become trapped in an underground mining chamber rocked by fierce seismic tremors.

When Lt. Colonel John Sheppard receives word that his father has passed away he returns to Earth but, once there, becomes embroiled in a covert and dangerous experiment gone awry.

Wanting to maintain diplomatic relations, Sheppard and McKay agree to accompany a precocious young princess on a rite of passage.

When an alarm sounds throughout the city, initiating a quarantine lock down, the Atlantis team finds themselves trapped in various sections of the city with no way out.

The Atlantis team successfully salvage a partially damaged Hive ship and in the process retrieve some critical information that may help in their war against the Wraith.

Now armed with the means to track Replicator ships throughout the Pegasus Galaxy, the Atlantis teams strives to eliminate the Replicators once and for all.

The Atlantis team's worst fears may be realized when a mysterious drone crashes into the city.

When McKay's sister Jeanie is kidnapped, the team returns to Earth to find her.

While trying to find her people, Teyla and the team meet a man with extraordinary prophetic abilities who predicts a frightening future for Atlantis.

Arriving on New Athos for an overnight visit, Teyla and Dr. Keller discover the entire settlement abandoned and their own lives in jeopardy from a primitive warrior tribe.

With almost everyone on Atlantis infected by an amnesia-causing virus, McKay finds himself zip-tied to his desk with cryptic letters on his arm and no memories of who he is or what has happened.

On his way back to Atlantis, Lt. Col. Sheppard and his jumper are taken prisoner by a rogue ship helmed by a beautiful but ruthless human commander with a secret agenda.

During an exploratory walk on a jungle planet, Lt. Col. Sheppard touches a glowing crystalline growth and unwittingly becomes host to an infectious energy form.

Ronon reconnects with a group of Satedans from his past who enlist the Atlantis team's help on a dangerous mission against the Wraith.

Lt. Col. Sheppard leads his team to the core of the Replicator home world on a high-risk mission to steal a ZPM, while Col. Samantha Carter, aboard the Apollo, races against time to locate the missing city of Atlantis.

When Rodney McKay realizes Atlantis has started shutting down artificial gravity and collapsing protective shields to compensate for a damaged power system, he turns off all non-essential systems. But when the problem persists, McKay is forced to collapse the shield to the point where it is only protecting Atlantis' main tower, leaving the rest of the city exposed to space.