In a weird way: The reason Anne-Claire is absent for most of Penny Arcade Adventures 3 after her brief appearance. It turns out that Tycho (our Tycho) is revealed to have abandoned his family's LongProject's original goal of stopping the universe's cycle of rebirth by way of destroying anything and everything that the Periphery can use as a seed for the next one. Instead, he seals Anne-Claire in a crystal in a secret corner of the Periphery, so that the next universe could be worth birthing. He's ashamed about the whole deal and Moira absolutely hates his guts for it, but on the other hand, the universe is coming apart at the seams at this point, and it's a lot better than stopping the rebirth of the universe for all eternity. And if you play the Beginning of the End DLC, it turns out that he's doing the same to You, your player character from Penny Arcade Adventures 1&2!
What's the enemy description for the final boss of Episode 4, a.k.a Tycho? "Thanks! It's been fun".
The Epilogue. Anne-Claire wakes up, as god of the newborn universe.
Alright, uncle. I'll take care of things from here.