The Pit is an ended story arc, with the main plot being the PAAB's mission to discover what The Order does/did with the bodies of those that oppose them. This story arc ended when The PAAB discovered The Pit and all the bodies along with it, fought and killed Saddam, and sealed the Pit.
After The PAAB discovered The Order, they believed some of the missing students were being help captive somewhere in the school. Addie deducted that Mrs. McNeil would likely know where they were, basing the assumption on Mrs. McNeil's prominince in The Order. Mallory, Austin, Hanna, and Payton volunteered to investigate her room.
During Principal Ray's inaguration, the four snuck to Mrs. McNeil's classroom and broke in. Mallory discovered files of student records in a folder labled "The Pit". Inside it were the records of many missing students. Payton opened Mrs. McNeil's utility clost and discovered a lever. After pulling the lever, the middle of the floor opened, revealing a deep pit full of the bodies of the missing students.
The sounds of The Pit opening attracted Saddam, who bursted into the room, golden machete in hand. Without saying a word, he charged at Mallory, who ran behind Mrs. McNeil's desk to escape. While she did that, Payton threw a coffee cup at Saddam, and then other little items, in an attempt to save Mallory and distract him from Austin, who attempting to sneak behind him. Saddam caught on and turned to kill Austin, but Austin pushed him towards The Pit. Saddam grabbed onto Austin's arm and tried to swing at him, but Payton hurled a monitor at Saddam, hitting his arm and making him drop the machete into The Pit. With Austin holding onto the door with enough strength to hold himslef and Saddam up, Hanna had enough time to use Mrs. McNeil's extension as a lasso and throw the cord around Saddam's neck. Hanna and Mallory tugged, slowly pulling Saddam off of Austin. When Payton joined in, the three yanked with all their might, throwing Saddam into the Pit, to his death. Payton then closed the Pit and broke the lever, preventing the Order from using it and discovering Saddam's body.
After this, the four fled to the bathroom and waited for the inaguration to be over. Although no members of the PAAB were killed, and a high-ranking official within The Order was slain, the discovery of The Pit and the bodies within dealt a major blow to The PAAB's morale.