1. Treason, Part One:
After
the success against the Wraith super hive, the city of Atlantis rests comfortably in the bay,
cloaked from view. Her first few days on Earth are busy, frantic, and largely
fruitless. Woolsey gives everyone some leave time while the city is prepared
for its return to Pegasus. While McKay
and Keller end up at Jeannie's, Sheppard shows Ronon and Teyla around San Francisco. One night,
McKay discovers a small asteroid heading for Earth with the potential to kill
millions if it strikes. As he quickly surmises that it must have arrived in the
wake of the super hive, he also realizes that Atlantis is the only way to stop
it in time. When the President decides to let it hit rather than risk
disclosing the Stargate program, McKay hatches a plan that may jeopardize not
only his own place in Atlantis, but Sheppard's as well.
2. Treason, Part Two:
Jeannie's offers of help in stealing the city are ignored
until Sheppard convinces McKay that they will need her. They decide to leave
Ronon and Teyla out of the loop to avoid risking their home on Atlantis, as well
as their ability to return to Pegasus. Major Lorne must make a difficult
decision when he learns of the plot, and Kavanagh helps without anyone's
knowledge. Atlantis, switching from cloaks to shields, deflects the incoming
tidal wave as the asteroid strikes the ocean, but the city is revealed to the
public in the process. Caldwell
assumes military command of the city and orders the arrest of John Sheppard.