So I talked my brain into reuniting with me, but when I get back to The Sink, the tank is empty, and the tank in The Forbidden Dome is empty too. Where did my brain go?

check the auto doc.

Nope Auto Doc only will swap heart and spine, brain must be in tank in order for me to swap it back in. WHERE DID MY BRAIN GO!!

He's probably in your inventory. I think you need to finish the main quest before he goes back in to you.

OK I get it, your brain is automatically placed back into your head. But the ending of the DLC lead me to believe otherwise. DOH!

Weird just finished the DLC again, this time the brain was back in the tank. Maybe a bug or something. But at least I got my brain back!