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John and Todd find a quantum mirror in an abandoned lab, and they are pulled through the smoky mirror glass into another version of Atlantis and Pegasus that couldn't be more different from their own reality. The Genii rule the entire galaxy, and Atlantis and the Wraith have built an alliance that is based on true friendship, something John has a hard time to believe.
To make their way back to their own world, they need to find a ZPM, but most of all, they need the help of the mirror New Lanteans and their allied Wraith. To add to the confusion, John also has to deal with the fact that the Commander of the mirror Atlantis is Colonel Aiden Ford, the counterpart of his former teammate - who is mated to mirror Todd and reacting to John's Todd in a way that makes John feel pretty jealous all of a sudden...