There's two possibilities regarding Cap:
1) In Unwired, p 164, it's mentioned that Cap's been spotted in a DIMR (Dunkelzahn's Institute for Magical Research) Matrix node. This makes sense, since if he got out of JackBNimble's memory space, he'd head there to a) ask for help and b) help with their Matrix.
2) In Runner's Havens, p 28, The Whampoa in Kowloon City are said to be led by someone named "The Captain", who no one has ever seen in person. Now, the Whampoa is also said to have the largest number of Technomancers in Hong Kong, and if Cap is back, I'm sure his abilities are more in line with a TM than an ordinary Hacker anymore.
What's true? Whatever you want, omae. Me? I like to believe it's both. He's working with the DIMR to figure out how he came to be how he is AND he heads up a tribe of Hackers/Technomancers in Hong Kong, fighting the good fight and training the next generation.