Heh, it's actually very proper for a ninja clan to have magic users (hidden arts) used to the clan advantage. It's rare they venture out of the clan-hold, but they can.
The back story was that he was sole survivor of his clan, returning with a small guard from delivering materials to an allied mage (off world) as part of a complex deal for the clan elders. Due to treachery the clan hold was decimated by surprise attack (a dragon and troops) but my mentor lived long enough to apport the clans sacred scrolls and book of records to me, with instructions to head back off world to save the clans honor (the scroll of deeds).
Lost the rest of the clan guards on the way out, but saved the scrolls & book. Now the GM was in a real mood, so when I figured I could at least hole up with our ally, I find out he's the dragon master! That led to a lot of role play just to survive.
Plus side, a very potentially powerful character once he's leveled up. Minus side, hunted by everybody and their dog <G>. Goals to survive and payback when I could. The bet I mentioned was I could take said character and outplay the group with defined role play, as they were pretty heavily roll play at that point. I'd say I was a bit arrogant, but figured I could pull it off and show them that using smart play worked as well as tank mode. The GM was pretty tired of a hack and slash crew, so he worked with me on pre-game set up stuff.
Classic ninja clans were spies and info gathers, seldom the black garbed killers of western movies. Great reason to make a business of buying & selling info and using my herbology skills to make stuff. I became the local apothecary, selling pain killers and compounds. Along the way two other players joined the extended group, playing assassin types who were sole survivors. Funny thing was, all generated similar stories under different GM's. We formed our own clan, with them as the muscle and I ran the back end.
Now the challenging part was the paybacks! Although the party never figured out I had a personal score with the evil mage whose tower we sacked <G>. I just claimed to have info on the inside from a mercenary I'd bribed, never admitted to being a guest <G>.
It took a lot of work by both myself and the other GM's who shared worlds to keep things fair, so in Hero system terms I had a ton of dis-adds to work off. Kept me busy, and focused on the goals. Was fun to retire many of those though, nothing says you can't hunt the hunters!
That particular character started in the early 80's and is still around, although the world he lives on is in twilight as the GM doesn't run any more. In fact I have most of the surviving world notes as she trashed most of her stuff. Sad. Luckily I'm a bit of a documentation type <G>.
I wouldn't recommend it for most players, as it could easily be unbalanced if the player wasn't goal oriented. Needless to say this is but the tip of the iceberg, with 15+ years of active character play and sever more as a grey eminence, there are a few stories ...