Mighty Avengers #12 starts out with the closing to Secret War, in which Nick Fury sent a group of heroes to overthrow the government of Latveria and then erased the event from their minds. He bid them farewell with a little bit of an apology, but an overall defense of his actions before promising to fade into obscurity forever.
A month later, Fury’s girlfriend comes to his hotel room in some remote Mexican city. He asks if she was followed, and then she gives him an update on S.H.I.E.L.D. matters, telling him that basically anyone he knew has been suspended. After a roll in the hay, said girlfriend decides to go out for some food. Fury goes invisible and follows her. He observes her having a conversation with a man in the alley during which she explains that she is slowly gaining Fury’s confidence. The goal is his private S.H.I.E.L.D. files. She tells the man to tell the Queen she’s in place.
She returns to the room to find Fury waiting for her with a gun drawn. He asks who she is. She bluffs and he shoots her in the head, splattering green blood and leaving a Skrull corpse on the floor. He goes invisible again and waits outside for the Skrull cleanup crew to arrive.
Two weeks later, S.H.I.E.L.D. Director Maria Hill awakes to find Nick Fury in her room. The two engage in some snappy banter before Fury tells Hill she’s not safe, and that she is surrounded by those who are looking to take her out. He advises her to make some life model decoys like he has. He also tells her that the first inkling he gets that she’s not what she’s supposed to be and that she’s not acting in the best interests of the planet, she’s not going to wake up. Then he splits, they try to catch him and he gets away.
Two months later, he finds Spider-Woman Jessica Drew. She chews him out for making her a Hydra and S.H.I.E.L.D. double agent and then screwing her over with the Secret War. Thanks to him bailing on her and S.H.I.E.L.D., she says, that leaves her “a secret agent of Hydra with no way out of it.” Fury tells her he needs her to go back to S.H.I.E.L.D. for reinstatement. He says he needs her eyes on the inside for the benefit of mankind.
He then talks to her about Skrulls, and how he thinks they’re inside S.H.I.E.L.D. He says he’s been watching her for a week, so he’s reasonably sure she’s not one. He tells her to keep her eyes open for anything off and report to him. She asks what he’s going to do, and he says he’s going to figure it out.
The book then cuts to a double-page spread of Fury standing before a wall of giant polaroids. A few — Spider-Man, Daredevil, Lockjaw and some blonde woman I don’t recognize — are circled in blue. A few others — Wolverine, Dr. Strange, the Sentry and Hulkling — are circled in red. I assume the blue people are folks who check out, and the red ones are suspicious.
I’m not quite sure when this exchange with Fury and Drew happens. She says she’s out of S.H.I.E.L.D. as a result of Nick Fury’s Secret War.
In New Avengers #1, she’s working on The Raft. By the end of that initial storyline, we learn that Nick Fury is already in exile and Maria Hill is in charge of S.H.I.E.L.D. Drew says in issue #3 she was yanked off her S.H.I.E.L.D. assignment for the Raft break-in, fearing she would be kicked out, but Captain America kept her on board. It doesn’t even sound like she was kicked out, much less kicked out long enough for the meeting with Fury to happen. So I’m assuming that she was kicked out of S.H.I.E.L.D. before the events of New Avengers #1 as a result of the Secret War, and that security assignment on The Raft was the demotion Fury anticipated.
Her conversation at the end of New Avengers #3 seems that it’s likely with Hydra, as Drew asks the mystery person “You want me to report back to you on this and on S.H.I.E.L.D.? That’s going to cost you.” We find out later in New Avengers that Drew was a Hydra double agent, and if the events of Mighty Avengers #12 take place before New Avengers #1 or #3, it’s established already that she was a known double agent.
The people she’s talking to say they weren’t responsible for the Raft break-in, though, which suggests that the shadowy character arranging the deal with Electro isn’t from Hydra. New Avengers #5 made it seem that Savage Land mutates were behind it all, but I think at this point it’s reasonable to assume that the Skrulls wanted that break-out to happen.