Not a bad episode but too much is covered in this one short episode.
We have a number of storylines. Lt. Colonel Sheppard's promotion and his visit to Ford's cousin. Weir's overriding the military command and forcing them to promote Major Sheppard to Lt. Colonel. Weir's marriage coming to an end. The selection of new members for the Atlantis team as they have a fully charge ZPM and the city can support more people now. Dr. Monroe and Dr. Lindstrom are killed aboard the Daedalus on its return trip to Atlantis after they discover a virus has been infecting the computer system. The discovery is then made by McKay and the rest of the crew but McKay recognizes it as Wraith in origin.
They try a number of times to wipe the virus without success and it takes over the navigation system and one of the 302 fighters. In the end Sheppard shoots down the fighter before it can send the Daedalus into the corona of a nearby star. This after a number of different solutions and perils are gone through.
In other words, too much going on for one episode. It's almost as if they were trying to wrap the first season and the last three parter with one episode so they can get on with season two.
Enjoyable with great acting and production values this episode could have been stretched out into two or shortened into one really good episode. Thanks for reading...