Annie lost her cool after her pen went missing, and forced the group to stick around in the study room until someone confessed. 

Everyone pointed the finger at each other leading to the point where they ended up in a group strip search, even going as far as cutting off Pierce's leg casts searching for the pen. 

Troy suggested a ghost came in and stole it, and the gang decided this was a more acceptable explanation rather than continuing to tear each other apart.

After they left, Troy's runaway monkey popped out from the air conditioning vent and stole something from off the table and returned to his nest which revealed all nine of Annie's pens, a "Troy and Abed in the Morning" mug and other assorted items.

When searching Abed's bag, Britta found a notebook proving has been charting the ladies menstrual cycles. Shirley's bag contained a pregnancy test and she revealed she's reunited with her ex-husband on Labor Day.  Abed points out that due to his expert record keeping, Shirley was ovulating on Halloween, not Labor Day.