Rising I and II
Dr. Weir and her expedition arrive on Atlantis. There are massive power failures, and a group leaves to explore Pegasus for a ZPM. They encounter both friend, the Athosians, and foe, the Wraith.
Hide and Seek
Dr. McKay finds a personal shield, and having had the gene therapy that gives the person the Ancient gene, is able to make use of it. Meanwhile, there is a shadow-like entity stalking the city.
Major Sheppard, his team, Teyla, Dr. McKay, and Lieutenant Ford, and two others are trapped in a orbiting stargate, when the acceleration pods on their puddle jumper do not retract. Sheppard also has a bit of a bug problem.
Major Sheppard's team has encountered the Wraith on five of nine missions. Dr. Weir's and Sergeant Bates's suspicions are aroused, and they interrogate the Athosians. Also, land is found.
Their puddle jumper with zero power, Sheppard and his team find a society where no one is older than twenty-five, and they say the Wraith have not been there for centuries.
Poisoning the Well
Dr. Beckett provides both knowledge and means to help research a drug that will help a population in defense against the Wraith.
Sheppard and team broker for a trade with the Genii. Or try to.
A planet whose stargate seemingly takes energy from the air, provides a way home.
There's a terrible storm coming, and the Genii learn that Atlantis will have only a small crew to guard her.
The Genii forces have commandeered Atlantis, and the storm is bearing a large wave straight at the city.
The Defiant One
Sheppard, McKay, and two scientists go to explore an Ancient satellite that was once used as the first line of defense against the Wraith.
A deadly virus is on the loose in Atlantis.
Perfect health, perfect society, perfect lie, in Rodney's opinion.
Before I Sleep
An old woman is revived from stasis and tells a fantastic story.
Under duress, Sheppard and his team decipher an ancient puzzle.
Letters from Pegasus
With the Wraith fast approaching Atlantis, the crew send messages home. Sheppard and Teyla are on a reconnaissance mission to gauge the threat.
Teyla has trouble sleeping, and it's found to be connected to the Wraith.
The Siege I and II
Though buoyed with reinforcements from Earth, the Wraith attack Atlantis, and the situation is desperate.