Belaran is correct, if a bit incoherent.

To expand upon his statement:
Deus brainlocks him just before the Shutdown, so that he cannot use the kill-codes. Later, Aneki is brought to Tibet and allowed in because he (or, more likely, his handlers) bore the Seal of the Green Gloves that he was left by Dunkelzahn. He is brought out when the Board of Directors for Renraku decided to try to get him into the Seattle Arcology and attempt to use the kill-code; IIRC, the PCs participate in the turnover in a 'monastery' in Hong Kong, but have to try to fight off Blues sent by Deus to kidnap him.
Either way, though, he winds up in the Arcology at the climax of the 'Brainscan' adventure series. Everyone gets plugged into the Machine, and at the 'endboss fight' Deus intentionally reverses the brainlock he'd done to Aneki and simultaneously info-dumps what he'd done on the guy. Aneki, in a fit of self-loathing and remorse, simultaneously triggers the kill-code (thus freeing for a few moments the portions of Deus locked into the SCIRE infotecture) and commits
seppuku in expiation of his failure to keep nearly a hundred thousand Renraku citizens safe. As he dies in the Matrix, he dies in the flesh.
And guess who gets blamed for his death? If you said 'The PCs', you'd be correct.
