So Olivia takes Lee into a manned security checkpoint, where she tells the soldier she needs an ID for Lincoln Lee. The sergeant gets Lee to put his hand on a scanner and then starts gathering his information: Badge number, blood type, medications, history of mental illness. Lee gets increasingly uncomfortable with the increasingly personal questions, but he answers them all (that's "no" on the mental illness, by the way). The ID card is fresh and ready to go, so I assume Lee has to do some sort of orientation? Well, maybe Olivia is the orientation. She leads him down a hall full of personnel. Everything looks brand-spanking new, and some of the workers are actually installing monitors. Suddenly a soldier escorts them through another set of doors, and then leaves them behind as an electronic voice says, "Initiate scan." The lights go red, there is a flash of white and some wind, and Lee is thoroughly discombobulated at this point. "Please remain still," nags the recorded voice.
Of course, this is where Olivia decides to jabber on about how she does know what it's like to have a hole in her life. "It's been there as long as I can remember," she says. Olivia, the machine said to stay still! Anyway, she says that when she joined Fringe, she somehow knew she would find answers. But that's as far as she's going to get with the personal revelations, because the scanner powers down and the access doors in front of them open up, revealing some sort of busy scientific facility, with dudes in white Hazmat-esque suits walking by. Directly across from them is another set of doors leading out. "What's beyond the door?" he asks, and Olivia says, "Sometimes answers lead to more questions." And sometimes not answering questions leads to the same questions getting asked again!
Not Lincoln Lee, though. He steps out into the facility, and we can see Peter's Doomsday device to one side, so I guess this is the hangar that houses it, filled with more stuff. Looking up, he sees cloudy skies through the roof on the other side of hangar, and looking back through the windows above the doors he just came through, blue sky.
But that's still not as freaky to him as what happens next. Olivia, only kind of sassier with long red hair and a -- what's that word -- smile on her face comes through the doors opposite. She chuckles when she sees Lee, but mostly ignores him and strolls over because Olivia's got something to show her. Olivia hands over the box: "It was powering a new form of shapeshifters," says Olivia, and Fauxlivia plays dumb. "Human shapeshifters. The ones we encountered before answered to Walternate. You were wondering why I don't trust you," says Olivia, who has the amusing big-sister role in this relationship.