User blog comment:Morganaforever/Thoughts on Merlin's finale/@comment-5674726-20121229015507

We never learnt why Aithusa allied with Morgana.

That's something that I'd have liked to know more about, especially after Sarrum's explanation that he captured Morgana by taking advantage of her love for Aithusa. That would imply that Morgana and Aithusa were reunited after Aithusa flew away at the end of The Sword in the Stone, Part 2, and developed a bond that was close enough for Morgana to endure two years of imprisonment, torture and goodness knows what else rather than risking harm to Aithusa by using her magic to escape. Sarrum must have known about her connection with Aithusa if he was going to be relying on it as his trump card.

Since she wasn't causing trouble for Camelot, what was Morgana doing before she was captured?

It's truly a pity that Aithusa can't speak because she was never able to say why she allied with Morgana.

One possibility is that, if Kilgharrah's prediction of Arthur as the Once and Future King uniting Albion, restoring magic, etc. was just one of a number of possible futures, Aithusa could have seen another future where Morgana would go on to accomplish great things, with the right support and encouragement. Kilgharrah nurtured the future he wanted by nudging Merlin along a path that would make him Arthur's protector. Maybe Aithusa was trying to nurture the future she wanted by protecting and helping Morgana as best she could.