We have a ninja adept in our group. Here's a rough copy/paste from the email sent with my build.
Concept was part street urchin with some ninja training. If you are a pure ninja, purge some of the non-relevant skills and use the BP to up the strength and unarmed combat, thrown weapons or blades skill. I made this character largely defensive and a high suprise/dodge pool. If you want to go offensive, decide if you want to focus on unarmed combat, blades, or thrown weapons and alter the powers to suit.
I felt defensive dice pool was more effective as it helps with surprise tests, ambushing targets and combined with judicious use of Edge and martial arts maneouvers, the ability to one shot people relatively nicely (if played smart). This is a personal bias though.
Finally, pick the Invisible Way Quality for 10BP from Way of the Adept and exploit the advantages offered in that PDF. I didn't have that book when I made this character.
So some of the skills aren't straight adept but I think it will become apparent what I was working for in a moment....
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--POSITIVE QUALITIES--
ADEPT 5
MARTIAL ARTIST (Ninjitsu -- +2 Infiltration) 10
--NEGATIVE QUALITIES-- (Swap out with 15BP of whatever, this was from the character's bio.
SIMSENSE VERTIGO 10
SCORCHED 5
BP COST OF QUALITIES: 0 (they negate each other nicely)
Attributes:
Body 3: Agility: 5 Reaction: 5 Strength: 3 = 120
Char: 1 Intuition: 4 Logic: 2 Willpower: 2 = 50
Edge: 3 Magic: 5 = 20 + 40= 60
BP COST: 210
Active Skills:
Stealth Skill Group: 4 40
Athletics Skill Group: 3 30
Dodge (Ranged +2): 4 18
Unarmed Combat (Ninjitsu +2): 4 18
Blades (Knives +2): 3 14
Survival (Urban +2): 2 10
Perception (Visual +2): 2 10
Pilot Ground Vehicle (Wheeled +2): 2 10
BP COST: 150
Knowledge Skills: (Total Points: 18) -- These can be swapped for whatever. Again, these are relevant the previous character's bio.
English: Native
Japanese: 4
Safe Houses: 4
Gang Identification: 4
ADEPT POWERS:
Improved Ability (Infiltration): 2 0.5
Improved Ability (Unarmed Combat): 2 1.0
Improved Reflexes: 1 1.5
Improved Ability (Dodge): 2 1.0 (or Penetrating Strike (2) and Killing Hands if you want to be more offensive than defensive with your bare hands).
Combat Sense: 2 1.0
MARTIAL ARTS MANOUVERS:
Disarm, Finishing Move, Iajitsu, Set-Up.
CONTACTS: - (Feel free to chop and change again.)
"O'Sensei" (Connection: 4/ Loyalty: 4) -16 BP
Mysterious Japanese Sensei. You think he's an outcast/disgraced ninja looking to rebuild a ninja clan within Denver by recruiting street orphans. You are his first student and he is most proud of your achievements to date.
"Gobble" (Connection: 3/ Loyalty: 1) - 8BP
Your snitch contact. He actually knows a lot of people on the street. You came up together and kept crossing paths. Like any survivor on the street, his loyalty must be bought and he will not risk himself for you.
Mr Feit (Fate as a street name just seemed kinda dumb to me) (Connection: 2/ Loyalty: 1) - 6BP
Owner of the halfway house. Use Slum Lord stats from Contacts book. Again, knows people and a lot of rumors and sees a lot. Don't expect much out of him though.
BP COST FOR CONTACTS: 32
EQUIPMENT: 8BP (40,000Y)
More than enough for a decent apartment, equipment, fake SINS, commlinks, weapons, etc. Go crazy.

NOTES:
This build:
Infiltration:
Agility 5 + Infilitration Skill (in Stealth group) 4 + 2 dice from Martial Art Quality + 2 dice from Improved Ability = 13 dice. That's before you use your 40,000 to buy stealth suits or anything cool.
Martial Arts:
Agility 5 + Unarmed Combat 4 (+2 if using ninjitsu-related moves) + 2 for the Improved Ability = 13 dice.
Surprise Tests:
Agiliy 5 + Intuition 4 + 2 Combat Sense = 11 dice (unlikely you will be ambushed. Ever.) Likewise, if you decide to Ambush someone? + 6 to that (17 dice... ouch. And they have to beat your Infiltration to locate you if you're hiding well...). Use Edge if you absolutely, positively HAVE to go first.
Full Dodge:
Agility 5 + Dodge 4 + Dodge 4 + Improved Ability Dodge 2 = 15 dice. Say no to being hit. If you do a Gymnastics dodge (cartwheel somersault flips or whatever, assuming space) from your Athletics Skill Group you add another 3 dice (18 dice).
Drawbacks to the Build?
I lowered the Magic attribute from 6 to 5. This means you lose our on Improved Reflexes 2 BUT that bought you a bunch of contacts though, including a sensei who can help train you over time (I figured you'd dig that and would like to re-write your story to accomodate if you wanted). This will work out better overall IMHO. You also have more Gear/Starting Cash, higher Strength and Intuition - which as you can see is useful for Ambushing people (key ninja skill). I got rid of crap like Ambidexterity, SURGEd and anything else that didn't fit the concept and just confused it. Add SURGE back in if you really want to, but if you do, stick to a theme (e.g. Gecko, Chameleon or something that is suitably ninja-ry). Plus as a ninja you wants to BLEND IN. Being a SURGEd character makes it almost impossible as you get Distinctive Style automatically and can never buy it off. Human works much better than any other race for that purpose.
Unfortunately your strength score really sucks, even with my boost of 1. If you sneak in on someone, you might want to use shock gloves or something as the damage value of those overrides your strength score, use Edge or switch to poisoned blades or something. If you chose the Penetrating Strike + Killing Hands adept power route, you can definitely do damage in a fist fight. -2AP to impact armor is nothing to sneeze at (better than Elemental Strike at this stage), even with Strength 3 as you have a lot of dice to roll and will be rolling first if you Ambush someone and making a Called Shot to an unarmored location. If you take those powers instead though you will lose two off all your Surprise Tests, which sucks as a ninja as that helps you ambush people and avoid ambush. Decide what you prefer. It's a tough call either way but whatever you don't get, I'd get with your next Adept power point. You can also use Set-Up and Finishing Move to take someone out unarmed. You do not want to take on multiple targets with this character. Leave that to Chris' character or something.
You can kill people and do some very nasty stuff but you are fragile. Your strength lies in striking while hidden. In a gunfight, Gymnastics Dodge if you're attacked behind cover or somewhere you can hide (Infiltrate) and Ambush the sucker from behind. You also have no ranged weapon skills. I did this deliberate but if you want, substitute Pilot Ground Craft for Pistols (Semi-Automatic +2) or rejig your skills to suit. Buy a gun with a smartlink too if you do that. I didn't figure you as much of a combatant though, apart from what your Sensei taught you so that's why I left it out.
You are not charismatic or liked much either, which means the easiest way for you to build contacts is to prove your usefulness (which is probably why your sensei would keep you around). You hide, you keep to yourself. You probably found the group through using the Matrix on your own so your personality issues aren't as apparent, but you got skills and ambition (maaaaaybe you want to take over O'Sensei's role one day... ? Once you've learned all you can at least... mwuahahaa...

. I took away crap skills like Locksmithing which gave nothing at a rating of 1. Better to default and take the penalty hit, or buy a lockpicker.
- J.