“Lockdown” is episode three of season eight of Stargate SG-1.
At the end of the previous episode, “New Order: Part 2”, Dr Weir had moved from commanding the SGC to running the Antarctic outpost, which is presumably when Stargate: Atlantis starts with “Rising: Part 1”, General Hammond had been promoted to head Homeworld Security, where he would oversee all related activity and O’Neill had accepted the rank of Brigadier General and command of the SGC (the last perhaps not the best fit of personality to job). O’Neill had promoted Carter to Lieutenant Colonel. The human-form Replicator, Fifth, had built his very own Sam Carter. Which wasn’t creepy at all.
The SGC is listening to a Russian team on the International Space Station, which is adjusting its orbit to avoid debris left over from Anubis’s fleet, when contact is lost. Something odd from a piece of debris enters the station, although no-one knows that as yet.
A new Russian colonel has joined the SGC, and wants to join SG-1. O’Neill, who is not coping that well with his desk job, declines. The colonel collapses whilst talking to Daniel and, when he awakens, has no recollection of what happened. Then Daniel starts behaving erratically. Fearing an infection, the base is locked down.
The colonel had a connection to a Russian officer who was on the ISS previously. The shadow that entered the station looked rather Anubis-like. Which is because it was.