What exactly did The Librarian do to Master Chief to keep him immune to the Composer?
You might want to say spoilers in the title but what she did to him is speculation at this point but I think it is a mutation she put on him.
I think she altered his genetic code in some way. Not sure myself.
Before had humans went into space but became unruly to the forerunners, they thinking the humans were rebelling destroyed and altered the evolution of the humans and made it so that would grow slower( forcing us into the nomadic stage), what she did was return him into his stronger, faster genetic code of there space born race, this is why at the end of the game they show his helmet coming off yet then cut away before showing his face.
Also spoiler tag Bro.
Except the Legendary ending has from the bridge of his nose and shaded eye, so very vague looking facial features.
She made him invulnerable to the composer by advancing his genetic code, as one of the guys above mentioned.
From what I can tell, when ancient humanity roamed the stars, they were fairly close to the tech of Forerunners, but ran into the flood. As a last resort, they invaded Forerunner space to evade the flood. When the Forerunners finally beat them back, the Librarian was tasked with tending to them. While on earth she altered the genetic code of humanity to allow for such evolutions as the Spartans. The evolution was to take place over time and culminate into something somewhat more than even a Spartan, but it was not complete when Didact was released, so the Librarian had to accelerate it. So far, we know the accelerated evolution has granted immunity to composition. This, in my opinion, can’t be the only advancement, though. That is what I’m curious about. What else is different?