The “shell” is what Rhinedottir calls the machine Albedo was created in, which is also used when he needs major modifications or healing that requires more than a potion.

Albedo hates it for three reasons; he has to use a feeding tube if he’s in it, he is paralyzed and suspended by tubes and wires, and it’s extremely claustrophobic.

This is how Albedo wakes up. In the shell with someone standing in front of him.