I just can't remember the name of this story. Jack, Daniel et al arrive at Atlantis by ship (they were a bit delayed by ship malfunction). They find an Atlantis that is in the grasp of the Trust. The story was, Stargate people turned up on a ship, were welcomed with open arms and then brutally took over. Turns out they were the Trust. Now when Jack and co turn up *in exactly the same way*, Altantis personnel are rightfuly paranoid and wary. The Trust imprisoned/tortured Sheppard and some of the Athosians. They claim that Sheppard is mutinying (or some such) but O'Neill isn't buying it however much he may seem to be paying lip service to the Trust people in charge. Rodney (and others?) were able to hide and have been trying to help the Atlanteans/Athosians against the Trust.
Jack is trying to get Atlantean people to trust him (possibly feels like Atlantis is talking to him), stuff happens, Trust get kicked out/flee, Daniel gets the title of best hostage ever, Sheppard gets kidnapped by Trust again (I think) and Atlantis and SG1 personnel have to co-operate to retrieve him?
At the end, the IOA is coming to inspect and Atlantis is still a bit paranoid. They have a number of refugees (including kids) on station and they are recovering/partying/swimming/have an Athosian ceremony of thanks when O'Neill brings members of the IOA down early. O'Neill knows if the IOA sees Atlantis as it really is the IOA members won't believe the Trust's lies that Atlantis tried to secede/breakaway/rebel against the SGC and IOA.
Please, does anyone know this story? It's all kinds of awesome and touching and heartbreaking and you can feel the desperation of the Atlantis people in the face of these odds.