Mirror-Agatha wandered in confusion for a while before finding that Klaus and Gil were still alive; she immediately went to them, and has been masquerading as Agatha since. Helen (along with Mell and Artie) rejoined the Circus, and has been masquerading as Agatha ever since. Sarah, who hasn't been out in the larger world for over a century, tagged along with the Circus, and has been masquerading as an animal (some sort of funky construct) ever since, and occasionally causing confusion by shifting into the Agatha form and others. Meanwhile, the real Agatha has been living as Maria.
A few people might remark on Agatha behaving a bit oddly -- that is, they are seeing Helen and don't know why she is acting so unlike Agatha. Certainly Krosp should be suspicious: he knows her best, and he's naturally suspicious, so he should have broad hints that she's acting weird. Zeetha should also have hints, although subtler ones, mainly relating to her suddenly being totally incompetent in training. Helen should not be enjoying the training thing -- it's probably her least favorite part of this disguise she has fallen into.
There are several possible outs from this plot, all centering on controlling the Mirror of Amagog. The best is to restore the Clockwork Crystal to its place -- at that point, any music, even simple humming, will control the Mirror. (At GM discretion, as seems appropriate.) The Silverodeon can control the Mirror directly, but only the Agathas have sufficient musical talent to do this. And Dingbot Prime can manually manipulate the Mirror's controls from the inside, but that's at the whim of the Dingbot. Note that all of this can also be used to send other people pretty much anywhere, including Skifander and Cynosure if they seem appropriate. Also, we need to make sure that all of these outs are sufficiently visible to the players.
Justin 1/14: Some tweaks: in Maria's original universe (the one that got melded in to create this one), she was following her version of Agatha into the Castle; so, in this "universe next door", she was in the room when it all happened.
Also, note that Artie got pulled into Helen's world a few weeks before they both landed in the GG world. So there has been time for the two of them to bond. He was sent there by an experiment of his Helen. The Victorian Helen was trying to replicate that, to send him home, when the crossover event occurred and she got pulled along in his wake.
Knowledge check: The person who best understands Amagog's workings is Silas. The ones who really grok this science best are Helen and Artie. The one who has actually operated this device (in her own world, using the Clockwork Crystal) is Mirror-Agatha. And the one with the most musical skill is Agatha. All of this should exist in the various character sheets, and we should be flexible about how it all plays out.
Characters In Game: Agatha Artie Baroness Gil Helen Krosp Sarah Zeetha
All Characters: Agatha Artie Baroness Gil Helen Klaus Krosp Mell Sarah Zeetha