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Shirley and Pierce's sandwich shop is chosen to replace the campus Subway, but a conflict ensues between the partners and Jeff has to argue on Shirley's behalf in Dean Pelton's version of court. Meanwhile, Troy is recruited by the Air Conditioning Repair Annex.

When the group's science project is destroyed, they decide to hold a trial to find the criminal, which a reluctant Professor Kane(Michael K. Williams)presides. While Troy and Abed believe they have discovers the perpetrator, Jeff soon realizes there's much more to the story than is believed.

Annie and Abed spend some quality time together in the Dreamatorium for a simulation of "Inspector Spacetime". The game soon transforms into an examination of not only the study group, but also a deeper look into Abed's mind and personality.

While Annie, Troy and Abed try to help Britta stay away from an old ex, Jeff and Shirley attempt to find out who he is. Elsewhere, Vice Dean Laybourne turns to Dean Pelton for help with his campaign to get Troy to join the Air Conditioning Repair School.

When a Subway open's in Greendale's cafeteria, Pierce and Shirley plot to shut it down. Meanwhile, Vice Principle Laybourne starts to turn Abed and Troy against each other while in the midst of another school-wise blanket fort.

Andre asks Shirley to remarry him and they set a date. Annie and Britta prep for the wedding while Jeff prepares the wedding speech. Shirley and Pierce present the idea of a sandwich shop to be added to the Greendale cafeteria to Dean Pelton.

The group tries to help Annie move in with Troy and Abed but things go awry when she becomes frustrated by their lifestyle. Meanwhile, Dean Pelton blackmails Jeff into spending the afternoon with him.

Pierce throws a party to celebrate his business success, but when his elderly father shows up, he puts a damper on the festivities. Meanwhile, Troy becomes a hot commodity for Vice Dean Laybourne and a janitor.

Britta fears someone in the group is a sociopath after her anonymous personality test turns up unsettling results. In order to find out who's disturbed, she and Jeff persuade the gang to tell horror stories.

As the study group sets to work on their first big assignment in biology - a terrarium - they are driven to distraction over how they should pair off to do their project. Elsewhere on campus, Chang patrols the school grounds looking for signs of trouble and imagines himself in a noir detective mystery.

Senor Chang settles in with his new job as a Greendale Campus Security Officer, while Britta is dealing with issues of civil disobedience after her friend is taken hostage in a foreign country. Annie is taking part in the Model United Nations competition and asks for help from the group to defeat her "friend" Annie Kim.

As the new school year starts, the group is back together and choice to take Biology. Jeff and their ex-convict Biology teacher instantly start off on a bad foot, which leads to strife within the group. Meanwhile, Senor Chang is living in the air vents and is given a new position of authority from the Dean, who has to make cut-backs due to the intimidating Vice-Dean's choice on spending arrangements.