What happened when the Phantom died?
For starters, it was to find out if it was possible to retrieve Phantom's body from Dead Lands, or at least some of his things. Quite often it was impossible to bring back the Phantom's body because the squad ran away from dangerous threats, leaving the bodies of their comrades behind.
Sometimes it was unable to return the body simply because monsters or anomalies destroyed it, there were cases when not even Phantom's clothes were left behind.
Then, upon returning to the Citadel, the Phantom's body would be sent to the military in their medical department. This was to check that the Phantom's body was not dangerous to others, viruses, unstable energy, the effects of some monster ability, and many other things that could cause problems.