We see a lot of Emily's life as Lauren, and time the she spent with Ian, who now has Emily hostage. There's a little boy involved - could he be Emily's and Ian's? Would Emily not only sleep with the subject of her earlier agent's job, and likely even care about him, but also have his baby?
No, the boy turns out to be only Ian's. He did want Lauren to marry him, so the three could be a proper family, but she says no. And later, after he's taken into custody - this is not now, but in the past - Lauren/Emily has Ian believe that his son was killed.
Ian, of course, always wanted to know by whom. And as Emily now tells him the story - still as Ian's hostage - it almost seems as if she was the one who killed the boy and his caretaker. She did hold a gun on them. The BAU team can see it's her by her bitten fingernails. But would Emily even for a second contemplate killing an innocent child?
Of course not! Indeed, Emily wouldn't kill anyone, unless that person was a homicidal maniac and a fatal shot was the only way to stop the murder of innocents. Emily just faked the deaths, as a way of giving the boy and his caretaker true safety (as in witness protection).
But now something happens that isn't being faked. As Ian and Emily struggle, he spears her with a big piece of wood. She's in very bad shape, rushed to the hospital.
JJ - back on the show for this episode to help with the case - comes out into the waiting room to give the team the worst news: Emily "never got off the table" - she's dead. But Hotch - the one person in the room who's not crying - walks out into the hall. Why? So the team wouldn't see him cry? No - they've seen him cry (when his wife was killed).
JJ joins him in the hall, and says something, which we don't hear. At that point it hit me - maybe she's telling him that Emily is not really dead. (Or maybe Hotch was part of this plan, all along.)
In either case, we see JJ meet Emily and give her papers and a new identity the next day. She deserves a happy life now. Great send-off for a fine character, and a fine performance by Paget Brewster.
See also Criminal Minds in Sixth Season Premiere ... Criminal Minds 6.2: The Meaning of J. J. Leaving ... Criminal Minds 6.3: Proust, Twain, Travanti ... Tyra on Criminal Minds 6.13 ... Criminal Minds 6. 17: Prentiss Farewell Part I
And Criminal Minds 5.22 and the Dark Side of New New Media
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