In the second season premiere, Jay wakes up in a hotel room seven months after the last entry, with no memory of those months. He decides that he's going to lay low, and get to the bottom of this.
Jay searches his hotel room for clues, and meets a girl named Jessica who may be part of the mystery.
Jay finds a video hidden on his hard drive entitled "noentry" and discovers that it includes a bloody rock and The Operator.
Jay meets Jessica again, and notices some weird camera activity when she's around. That night, he hears weird noises coming from her room, and tries to confront her, to no avail.
Jay goes looking for the place shown in Entry #29, but finds a mysterious man following him. Later, he talks to Jessica again, where she reveals she may have been affected by The Operator.
Jay gets confronted by Jessica, who is also having memory loss. The two decide to meet in her room, while Jay uploads the entry in case something happens.
Jay goes back to Jessica's room, but finds her missing and the combination to the safe in his room. After grabbing things from the safe, the Masked Man appears.
Jay begins going through the tapes, starting with one from April 21st, which shows him going to the return address of the package he was sent.
Totheark returns with a video of torn-up pictures of Alex, and the words "you are broken" and "you cannot be fixed."
Jay goes back to the building, with Alex, and the two meet Tim, who turns out to be someone they know.
Totheark video which has a person narrating in a very distorted audio format.
Jay finds corrupted footage at the end of the tape from the last entry, and finds out that Alex was the one who sent the package to him.
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The channel is hacked again, and we see birthday footage of Alex, with some strange things put into the tape.
Jay finds an unlabeled tape that has him and Alex walking through the woods, while Alex tells a story about those woods. Jay is uneasy about how Alex acts.
Jay gets a call from Alex about a week after the last time they met, and Alex says to meet him at Rosswood Park. Later that night, outside Jay's window, a man is seen looking in at him.
A totheark video that shows he was the one outside Jay's car, and that something sinister is going on.
The day after Jay gets the call, he goes to Rosswood Park and can't find Alex. As he walks around, he encounters The Operator.
A totheark video that shows images implying the Masked Man was in the forest with Alex, and the message, "Did you see me? I saw you."
After 15 minutes of silence on the tape from Entry #40, the camera is picked up and taken back to Jay's car, where it's revealed that a masked person was the one who brought it back.
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Alex makes it to the park and finds Jay hysterical, after being in contact with The Operator. Jay later finds his camera in his car, with no idea of how it got there.
Totheark video which includes the ominous message: "So much more than time has been taken."
Alex and Jay go back to Amy's house, looking for Amy, but find nothing. Later, Alex goes to the woods alone and meets the Operator.
Another totheark video, posing some questions about who he is and who you are.
Alex is alone at home when he starts coughing, drawing pictures involving the Operator symbol, and seeing the Operator himself.
Alex is at home, when he suddenly chases after a masked man outside. The masked man overcomes him, when it's revealed that two of them exist.
Jay follows Alex to his house and sneaks inside, finding a tape before Alex catches him. The Operator appears, and Jay escapes, not without taking both the tape and a key.
Totheark video which asks the question: "Do you know what he did?"
Alex confronts Jay about the break-in, which leads to Jay and Alex splitting up, but not before Jay gets Jessica's phone number. He calls Jessica, who tells him that Alex has apparently found Amy.
Jay starts following Alex, and eventually discovers that he's been going into the woods, and to the same tunnel from Entry #29. He decides to look at Alex's footage to get a clearer idea of what's going on.
Totheark video that tells the viewer to "be silent", and that "this is the best part".
Alex goes to the tunnel as shown in Entry #48. The man in the white shirt follows him and when Alex sees, he kills him. The Operator takes the body. Alex tells Jay to meet him at Rosswood Park.
Totheark video connecting Tim and the Masked Man. "How much do you hate? It is not enough."
Jay and Alex go to Rosswood Park, but end up with nothing. Jay sees the Masked Man. He gives chase but is unsuccessful. The next day, Jay sneaks into Alex's apartment again and grabs the tape that he didn't grab the last time.
The tape that Jay stole ends up being more footage from Marble Hornets. The truth about what happened to Brian comes to light.
In the second season finale, Jay finally pieces together the last days of his 7-month gap.