I don't remember if this was a book, manga or anime, but I recall that the story started with people on a ship (submarine?). There was a fight on the ship and later they arrived and went through a big metal gate into a city.
Inside the city they had to fight monsters (or evil people?). I remember a there was a doctor of some kind. I'm also sure that the characters had special abilities.
I was living in Germany when I saw/read this and it was probably over 5 years ago.