The story follows his gradual loss of agency. He can no longer tell which thoughts are his and which are inserted by the hack. Other hackers who’ve encountered it show similar symptoms: fragmented personalities, obsessive behaviors, and a strange collective knowledge.
It sounds like you're referring to a short story by Michael Swanwick (published in Asimov’s Science Fiction , 1993, later collected in Tales of Old Earth ). homo hack
Initially, the hacker sees it as the ultimate key: with Homo hack, he can rewrite financial records, erase identities, and control information flow. But as he experiments, he realizes the code has a will of its own. It begins rewriting him — not his files, but his memories, desires, and sense of self. The story follows his gradual loss of agency