After three weeks, Olivia is finally ready to check out of the hospital. Upon her leaving, "evil Charlie" watches her go (remember that Charlie was killed by a shape shifter that is now pretending to be Charlie) whose assignment is to get Olivia to confide in him about what happened with William Bell. Walter has been investigating her disappearance and still can't explain what happened to her during the time she went missing from her car accident and when she flew through the window. One thing is for sure: she came back with heightened senses that help her to solve the latest fringe case. Olivia jumps right back in -- ready or not.
When a construction worker goes missing in Pennsylvania, our Fringe team arrives on the scene following a lead that this is the seventh disappearance with the same circumstances. While investigating, Walter secures some blue goop, while Peter talks the brusque local Sheriff, C. Howard Golightly, into releasing the town's citizen files into his and Olivia's possession.
Later, Walter discovers the blue goop he collected at the crime scene is both a paralytic and partially comprised of human DNA. Meanwhile, while reviewing the townspeople's files, Olivia ties one man to the scene all of the disappearances: Andre Hughes, formerly a doctor.
Peter and Olivia head back to Pennsylvania to question Andre. Olivia swears she hears someone else breathing in the house. After she's checked the house for others unsuccessfully, they eventually bring Andre in for questioning. Andre reveals an important bit of information -- his wife died giving birth to their child some years ago. But even as Andre further convinces our team of his innocence, he refuses to let them draw his blood so that they can see if his DNA matches that found in the blue goop. This refusal makes our team suspicious. Later, in his cell, Andre crafts a noose out of the mesh lighting wire and hangs himself.
Let's not forget, while attempting to solve a case, Olivia is STILL recovering from her accident. During a follow-up visit with her doctor, Nina Sharp shows up recommending that Olivia see a specialist to help her recover after everything she's been through. Olivia accepts the card of a Sam Weiss, whom Nina thinks can help Olivia.
At Walter's request, the team exhumes the graves of Eve line and Baby Boy Hughes only to discover that the baby boy has burrowed his way out of his grave. Back at the lab, Walter performs an autopsy on Eve line's remains only to discover she had advanced Lupus -- a disease that would have prevented her from having children. Walter determines that Andre, a former doctor, altered his baby in the womb so that it could survive in spite of its mother's Lupus. The baby somehow survived. Olivia tells them that she is certain she heard someone in Andre's house when they were there earlier.
At Andre's house, Olivia and Peter search the house and eventually make their way to the basement where they find a tunnel (like the one we saw burrowed under Baby Boy Hughes' coffin) in the wall. As Peter searches for a shovel, Olivia is attacked! She is dragged violently into the tunnel by the sickly looking beast, where we find our victim from the beginning and Officer Golightly.
Peter comes to the rescue and wounds the creature, which borrows its way out only to collapse in the driveway. A car comes crashing through the earth, crushing the beast. When a swarm of FBI agents arrive later, they discover a number of bear traps. Andre knew he was responsible for the killings and was trying to capture his creation before it took more lives.
Back at her apartment, Olivia relaxes in a hot bath. She begins to hear things again, but this time it's worse. She can hear everything: an insect as it crawls along her windowsill, drips from faucets, bubbles popping, neighbors speaking, bugs flying, traffic, the disturbing hum of the overhead lights. This is enough to force her to take Nina's recommendation about Sam Weiss.
Olivia shows up at a bowling alley, where Sam Weiss works. He's been waiting for her...
Charlie returns to the mysterious typewriter shop to get his latest instructions. The typewriter sends him a message that reads, DO SOMETHING TO HELP OLIVIA REMEMBER WHAT HAPPENED.