Back in 2000, a small independent company named Io-Interactive released its debut, Hitman: Codename 47, which proved to be the first of a successful franchise. In 2006, Io was purchased by Eidos. In 2009, Eidos was purchased by Square-Enix. So Io is now a wholly-owned subsidiary of Square-Enix, and thus, the Hitman setting is part of the Disney/Square-Enix Empire in my campaign.
(It's fun to note, in passing, how the consolidation of entertainment companies in the real world parallels the expansion of the empire in my campaign, but that's an issue for another post.)
Except for their shared ruthlessness, Agent 47 has nothing in common with Captain Crocodile. The latter is a very prominent part of the Disney war machine, whether leading troops from the front, or heading the administration of a conquered world. 47, on the other hand, should be all but invisible.
As far as actually describing Agent 47, well, there's not that much to it. He's a mercenary assassin, a contract killer, a murderer for hire. He's genetically engineered (or something) for maximum ability. He occasionally shows flashes of morality, but never so much that it actually interferes with his job. His role in service of the Mouse Emperor is pretty self-evident. Once the player characters attract too much attention, Agent 47 gets sent after them.
The great thing about Agent 47, from my perspective as a GM, is that he could be anywhere, and can strike in any fashion. Any world that has humans could have Agent 47 skulking about in stolen clothes, ready to slip some cyanide in a drink or unleash a volley of .45 ACP bullets.
Possible Aspects (NPCs only get one):
The Contract is Everything
(images copyright Io Interactive, or possibly Square-Enix)