Michael sent Adam's soul up to Heaven with his mother before using his body. When Michael said "Adam's not home right now," he meant it. Adam never got stuck in the Cage, that's why we never heard anything about him after "Swan Song".
Ouat is the best show. The creators of this wonderful tv show must be proud of theirselves for going up to 100 episodes because I think that's rare in a tv show. I am also glad that I am so attached and have a huge crush on Colin O Donoghue. If I hadn't watched this show I would of never known such a great guy like Colin