I found this story confusing. Was the drinking, drugs and dyslexia part of her cover story, part of the "template"? If so, a drunk, coked-out dyslexic super-agile is not an effective crimefighter. (I half-expected that she was going completely paranoid when she thought the guys in the club were connected with the kidnapped baby.) Furthermore, if she is deep cover, why was there no emergency procedure for her to make contact, like a code word or secret 1-800 number?
I get the idea that the protagonist is getting screwed over by the organization she works for, but it seems so blatant and so pointless that I don't know why she doesn't quit. Unless that's part of her mind-control template too.
As a side note, I'm wondering about something I've noticed in the Union Dues stories, Mur Lafferty's Playing for Keeps, the Secret World anthologies and other prose versions of the superhero genre. The authors keep making their superhumans members of large, bureaucratic, state-sanctioned, hierarchical organizations, with lots of Silver Age trappings (skyscrapers, jets, etc). They're bureaucrats with superpowers, not superheroes, closer to Jack Bauer than Batman.
You can compare this with Neil Gaiman's Eternals for Marvel and Grant Morrison's Seven Soldiers of Victory, both of which try to put the "hero" back in "superhero" by rejecting realism and investing characters with mythic significance and making them players in vast cosmic, Jack Kirby-based mythologies. What's lacking in the Union Dues stories and the other works cited above is that sensawonda, IMHO.