When reading your other thread I got curious about the Shadowheart conversation near the créche and fired up a save game to check it out. The dialogue goes as follows:
Shadowheart: "I can't believe I'm actually venturing into a gith stronghold again - voluntarily. This had better pay off. [...] I've seen them at work before. I wasn't alone in my mission - all those who were sent with me were slain by githyanki blades. They must want that artefact back bdaly, if they're dispatching red dragons in puruit of it. But we cannot afford to lose it. I wish I'd never been sent on this mission. It had better be worth it."
Tav: "I'm curious about that, myself.
Shadowheart: "You'll have to live with that curiosity for now, I'm afraid. Let's just concentrate on ridding ourselves of these tadpoles. All will be revealed in due time. I hope."
In the Cloister of Sombre Embrace you can find a list with names of the people who were on the strike team and what their role was. So it seems that Shadowheart went into a creche with her strike team (sent out by Viconia) where they stole the artifact before she was tadpoled. She was hunted by the Githyanki and during her flight she somehow got snatched up by the Nautiloid and was tadpoled there. In proximity of the artifact the Emperor managed to break free from the Brain's influence and started following his own agenda.
(An interesting question is if our heroes were tadpoled by the Emperor before or after he broke free. We know Durge was the first to be tadpoled, but the others? Did he create his own strike team to do his dirty work? But I digress.)
