I’d probably use Animus, a derivative of Black Seven. The latter is an rpg based on stealth-focused video games like deus ex, alpha protocol, thief, metal gear solid, and others including assassin’s creed. The former is a variant that is focused specifically on replicating games like Assassin’s creed. It’s a surprisingly simple system, and has an excellent mission creation system. If you are pretty good with the system hacking you could easily port the concepts over and use your favorite resolution mechanics. I’ve been doing it with Mythras and it works quite nicely (should work very smoothly with any d100)
Thanks for all of the suggestions everyone! I've given the GM the link to this thread, so hopefully he'll take a look at what you all recommend.
I don't know if it changes anyone's recommendations but in talking to the GM yesterday he was hoping the game focus would not be on group combat but rather quick focused strikes, then fading into the shadows. And each player would have a specific specialty (poison, the brains, knife throwing, etc.) that would give them the spotlight depending on the type of assassination that was being done.
I think you ought to check out Blades in the Dark. It has everything you need, designed and focused on a crew of criminals carrying out jobs. Your crew has it's own character record, while each of the roles is given it's own space, whether you're a killer, an infiltrator or more of an alchemist.
You'll need to tinker with the default setting, but that's okay.