WMG: Black Cat
The Doctor is actually a younger version of another Doctor.Let me list the similarities. Scary Shiny Glasses? Check. No Name Given? Check, except if you manage to get Cave Story's good ending. Mad Doctors? Oh, yes. Considering how both series have a good deal of magic and technology, it's not too far-fetched to assume that Cave Story actually takes place in the not-too distant future, where the Doctor was able to live longer by using his medical prowess. He pretended to atone by becoming a medical doctor, until he heard of a certain Momorin Sakamoto's plan to go on an island with a certain Artifact of Doom stored inside...
Like Eve, Train is a result of bioengineering, and is more catlike than meets the eye.He has golden eyes with slitted pupils. He's a great jumper. He likes high places. He's strong. He can sneak around like a phantom. He's super fast. And he LOVES milk. He may actually be part cat.
Train and the Huntress are best friends.The Huntress from Birds of Prey and Train have a lot in common such as fighting a battle with in themselves every day to love instead of kill. Not to mention the whole animal thing. In the pilot episode the villian of week says to hunter "Why bother getting revenge for the death of your mother. It's not like it'll bring her back." In the anime Creed is trying to get shot by Train but Sven says "I don't know the history between you too but killing him won't bring Saya back." In the episode Three birds and a baby the Huntress doesn't mind Guy being a warrior but does mind him being an assassin. Train is an ex-assassin who doesn't like that lifestyle. Maybe they could get along.