The Man in the Planet is a human version of the baby preparing revenge on Henry.
It's Mary's dream, as her sleeping mind tries to understand why her husband lost his mind and killed their perfectly normal baby.
- The almost-abandoned city that Henry lives in is one of the few standing settlements on a barely-habitable planet that's been terraformed just enough that a handful of humans can live on it. People eat weird synthetic chickens because the nearest real chickens are light years away.
- The Man in the Planet's planet is actually the planet that Henry lives on. The Man in the Planet is either an engineer involved in terraforming (who was presumably mutated during his time on-planet,) or a vengeful alien trying to get revenge on one of the intruding humans by making his life hell.
- The Baby's weird physiology is either the result of mutation from exposure to extraterrestrial chemicals that the human body isn't equipped to handle, or because Mary was actually impregnated by one of the native almost-extinct aliens without her knowledge (perhaps the Man in the Planet.) Ditto for Henry's hallucinations, which could be caused by a combination of exposure to the chemicals and cosmic radiation.
- It is one of the possible existences Shinji imagines for himself. The man in the planet represents Gendo, pulling the strings of instrumentality. That's why the planet explodes at the end; Instrumentality is rejected by Shinji and ends. The woman in the radiator represents Yui, and that's why she is happy at the end when everything fades to white; Shinji rejected instrumentality. The Baby is a horrific manifestation of Shinji's fear and insecurity, and only by overcoming it, or "killing" it, can he escape.
Being executed for infanticide, he has a distorted flashback to the events that led to his crime. The Man in the Planet is the executioner, hence his sinister lever-pulling bookending the film. This also explains all the disturbing imagery involving electricity, and Henry's electric-shock haircut.
...i need my medication...