The feds were working with Rife. The evidence includes (not in chronological order): The EBGOC/RARE package to the US for which YT was specifically (they want to know her name, doesn't matter if it's unreturnable, "you're YT?" when she delivers) needed (ch 41), due to interest in her ... because they know she is working with Hiro the hacker and probably also the mafia, and she escapes the 'falabala' park twice (the technology for that intel is easy), and she must know something about the Plan because she destroys her mother's Fed computer (mom's a Fed programmer), Ch. 37 reveals that YT's mom's job concerns a program about which she knows nothing except that there are a lot of people working on it. Then her mom is interrogated concerning her daughter's behavior. Later YT sees a RARE helicopter on the raft, and the President of the US gets in it with her once she's kidnapped. Doubtless there is more.
It is clear that YT is a small fish that is interfering in Rife's plan. She is young and relatively inexperienced, and thus easy to take in the course of her Kourier duties. Once captured by the Feds she is transferred to another of Rife's tools: Wayne's world. As it were. This answer is fairly good.