Portal and Half Life... oh, wait.
Okay, really now, seriously. Halo... and Katawa Shoujo. Post Halo 3, of course, so the Elites (Sangheili) are allied with humans. Think about it. You know it makes sense.
Rin would make a pretty awesome spy for ONI. She's eccentric enough that no-one would believe her if she came close to blowing her cover. She'd be pretty useful against the Insurrectionists, as no-one would suspect her. Emi would make a great soldier, her speed would be useful in battle and she could easily outrun most ODSTs. Not to mention she has an advantage being legless if she wanted to become a Navy pilot, since (real-life, this) people without legs are less likely to black out or lose mental faculties from the high G-forces in high altitude flying and dogfighting. An actual fact, used to great effect by amputee pilots in WW2...
Shizune would be a good commander of forces, probably end up as Master Sergeant or something. Or a high-ranking ONI officer. She also wouldn't be the only mute in the series (Lucy from Ghosts of Onyx/Glasslands?). Misha would have to translate for her, of course... Lilly wouldn't exactly be a good soldier, being blind, but she'd have an advantage in ONI again from her intelligence and her adaptability. She could probably get implants anyway in the Halo universe to give her sight too. And Hanako would get on well with the Sangheili, who would no doubt see her scars not as a problem but more as a sign of honour (we're talking about a race that merits warriors and battle, after all...).
There are plenty of disabled soldiers too who've probably had to leave active service in the UNSC after their injuries stopped them from fighting. Plus, all the near-dead, disabled SPARTAN-II washouts being kept alive by ONI medics for ONI purposes. They would all fit in well at Yamaku Academy. Yep, I'd say the two universes could easily cross over. Who's to say that Yamaku isn't actually located in a future Japan in the 26th century, huh?