He was injured and like many of the patients, the hospitals couldn't help him. The Monk was frustrated with him because the treatments didn't seem to be working, but he was unaware that Mr Francis was actually a telepathic telekinetic. The Doctor speculated that the treatment, faced with the choice of trying to heal Francis's body or help him in some other way, chose to enhance his mind.
As a result of his enhanced mental state, Francis was essentially immune to the mind-altering side-effects of the treatment that drove the other subjects to try and infect the rest of the human race. He used his telekinesis to help the Doctor cure Jo of the mutation by injecting her with the Doctor's cure, while his telepathy allowed him to project himself into the Monk's TARDIS via its telepathic circuits. While he resented the Monk for turning him into a freak, Francis resolved to protect the Doctor and Jo from the other patients. The mental strain of telekinetically stopping the transformed UNIT soldiers shooting at the Doctor killed Francis, with Jo musing that even if Francis wasn't a good man, he had been trying to be better. (AUDIO: The Rise of the New Humans)