WHAT WE KNOW: Aeryn is presumed dead. She is frozen. Salis revealed in Durka Returns that Durka was put in a state of cryonic suspension for over a hundred cycles to subdue the mind cleansing. The Nebari have superior technology to everyone else we've encountered so far, save the Ancients.
WHAT I SPECULATE: This, my friends, is where the Nebari come into play. Now, we know they mind cleanse people, and we KNOW that the people have to be frozen for it to be permanently done. OK, got all that in your memory? Good. Now, what if the Nebari somehow find out about Aeryn, and her connection with a certain young female Nebari who is supposedly allied with the resistance--we'll call her Carol. I think that Season 3 begins with the Nebari, in effect, hijacking Aeryn's corpse. Then they revive her, and put her through the ol' mind toaster. Then the new calm, happy Aeryn is given instructions of what to do (find Carol, bring her back), and Aeryn reunites with whatever crew of Moya she can.
In this scenario, Aeryn will be successfully revived with some minor damage to her mind. Now, there's a fix for that. Problem? Nobody knows exactly what it is... except Rygel. Aren't you glad they didn't get rid of him? Bigger problem. Rygel got another ship. He's nowhere to be found. Uh oh! Time to do some step retracing. "Pilot! What happened just before Durka broke his mind cleansing? Heck, if you could figure out how to get here to the Tavloid planet, you should know what happened to Durka!" And Durka's incredibly brief reappearance in LGM2, combined with the noticable Head-On-A-Stick trophy even enforces my theory. I don't think they would bring Durka back only to get rid of him so quickly. There was some significance buried deep behind Durka's return, and I think this is it.