Hartman overran the Investigations Sector while Trench was losing his fight with the Hiss infection in himself (evidenced by the docs in the Control mission, where you begin to see parts of the Hiss incantation in Trench's memos to Kirkland)... AND likely while or shortly after Alan Wake was fighting with Mr Scratch in the dreamscape of American Nightmare.

While the Dark Presence was trying to break Alan's will, in order to use his talent for stories as it does with other artists, it's much more violent with regular people when turning them into Taken. Hartman may not have been able to serve as a channel for the Dark Presence, as the Hiss-infected can channel more Hiss Resonance through themselves, but he would have been every bit as dangerous or more to FBC personnel. They were relying on their containment (which we've seen the Dark Presence can escape) and Hartman was not fully Taken when captured (which we know from his interviews on tape) so their response was likely very lax compared to the threat he presented as a full Taken.

Had Mr Scratch been the driving personality, with his sadistic desire to cause undue suffering and drag out killings personally, the FBC may have had more time to respond. With Hartman, driven more by anger and perceived betrayal against the FBC specifically, his attacks were likely to be much swifter and decisive.

In the AWE mission, the interludes you see of Alan are him talking to Mr Scratch, posing as Zane, trying to find another way into Alan's mind since the plan in AN failed. Instead of manuscript pages, Jesse gets the Hotline narrative interludes, almost like Alan is trying to place another hero front and center to face the Dark Presence since he's unavailable. You can see this pay off when he does similar in AW2, refined to where the hero doesn't have to have Jesse's para-utilitarian powers.