Phantom's messed-up state happened because of the special collection of weapons, the armory, that was sent out. Rattan has been working on these weapons for years. The last five years has been full of tricky politics and secret plans, and Rattan was right in the middle of it.
Everyone important was watching Rattan. With years passing by, it was hard for them to hide their distaste for Rattan's plan to help the Ratmen so there was no way they would have let the weapons he crafted get to the ratmen, especially with all the secret tricks Rattan had built into them.
This is where Phantom, whose very essence was cursed with the ironically revealing moniker "Spotlight Phantom," proved invaluable. His unparalleled ability to remain hidden, to vanish into the periphery, was his greatest asset. To ensure Rattan's grand design came to fruition, Phantom had unhesitatingly offered himself, sacrificing portions of his own being.