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I've just joined a TMNT game and we're all making characters, but some of us want to play Human characters alongside the Mutants but we aren't sure how to make them to fit in well with the mutants. What book/ruleset would be best to use alongside TMNT for this?

Edit: A second question as well. The Human characters in Question are Foot Ninja, what would be best to represent that build? We're looking at N&SS as well, but the Ninjas in there don't really fit the Foot Ninja style in that they're all sequestered monks with like no worldly experience or skills what so ever. We were looking at some of the other stuff, but have no idea what the best Martial Art for something similar would be.

A really effective way to do this in the old TMNT game that I have found is to simply build the character like they were a mutant for the skills (foot ninja)
but roll 3d6 for all stats, start with a base of 30 SDC and they of course automatically get 'full everything'

Transdimensional TMNT has a human base animal.

The decision to limit exclusive martial arts to Dedicated Martial Artists really made the revised edition of Ninjas and Superspies a lot less flexible. If you ignore the exclusive restriction and build an Operative Agent with ninjutsu, I think it can still meet your needs. You could also swap one or two of the martial arts powers to gain basic skill programs, if you want to stick with the Dedicated Martial Artist.

Really, any other Palladium game book will do for a normal human character. Though I would recommend Beyond the Supernatural, Heroes Unlimited, or Ninja's and Super Spies.