John Sheppard and his team on are their way back from a possible location for an alpha site when the puddle jumper experiences difficulties, they manage to get it under control and make it back to Atlantis only to realize the problems with the jumper are now happening in the city. McKay seems sure that the problems are not be related, Atlantis then loses all power apart from one laptop which begins to speak, it's none other then Dr Elizabeth Weir The following will give away the full story
After the replicator home world was destroyed it gave Dr Weir and her Replicator "Friends" a chance to study their goal of ascension, they believe they obtained their goal only to end up trapped in subspace, travelling the galaxy in search of a race that was advanced enough to create them new bodies, weir has no choice but to seek out Atlantis,