The gang works on their evolutionary chart in the study room for Professor Duncan's anthropology class. Dean Pelton swings by with an adorable puppy in his arms to remind the group that the local animal shelter is having a puppy parade in the quad that afternoon. The Dean wants the whole study group present. Just as everyone gathers their things to head off on their merry way, Annie can't find her purple pen with a gel grip and stops the whole group from leaving the study room. In fact, Annie freaks out, letting out a bloodcurdling scream, all over her purple pen gone missing.
Annie proves to everyone that her purple pen was on the table a mere 10 minutes before. She took a picture of it on her phone. Britta tries to leave for her photography class, brushing off Annie's freakout, but Annie stops her. Annie asks if they can all have a look in Britta's bag since she's so quick to want to leave. Britta, claiming an invasion of her civil liberties, makes a speech about her constitutional rights. After getting annoyed with everyone, Britta turns over her bag and dumps its contents onto the study room table. No purple pen to be found, but Jeff does comment on the packet of condoms Britta apparently carries around.
When Dean Pelton announces over the loudspeaker that the puppy parade is starting, everyone gets up to leave again. But this time Britta stops them. If she had expose her personal belongings to prove her innocence, then so do they. Pierce thinks Troy has the pen. Troy thinks Pierce stuck the pen down one of his leg casts. Britta thinks Shirley might have it. With everyone blaming each other, Annie enlists Jeff to run the investigation. Before starting the search, Jeff gives "the thief" an opportunity to come forward, but instead, Pierce uses this opportunity to blame Jeff. Now Jeff's pissed and decides to lock down the study room, not letting anyone out until the pen is found. He even cancels his date. The gang is doing a bottle episode.
Jeff sits at the head of the table as he administers a search on everyone's bag. Troy, as he said, doesn't even have a pen of his own. In fact, Jeff finds only a neck pillow in Troy's backpack. After Troy, it's Abed's turn. When Jeff opens the bag, Britta grabs his notebook. Jeff sits at the head of the table as he administers a search on everyone's bag. Troy, as he said, doesn't even have a pen of his own. In fact, Jeff finds only a neck pillow in Troy's backpack. After Troy, it's Abed's turn. When Jeff opens the bag, Britta grabs his notebook. Abed has created a calendar calculating the girls' menstrual cycle for his personal use. He explains that when he realized Shirley, Annie and Britta were more sensitive to things he said at different times during the month, he started charting their reactions. He started getting positive results by approaching them differently during certain times in their cycle, and everyone benefited.
Shirley is the only one left with an unsearched bag. Abed tells her its time to dump the contents of her large bag onto the table and end this. Shirley refuses. Annie, Britta and Troy approach her like detectives. When that doesn't work, Pierce fakes a scream, grabs the bag and they're done with it. Then Troy grabs the bag from Pierce and hands it over to Jeff. He dumps the contents onto the table. Britta immediately sees a pregnancy test. Shirley explains that she and her ex-husband recently reconnected over Labor Day. But Abed lets her know that she couldn't have conceived Labor Day weekend. According to his chart, she wasn't ovulating, but she was during Halloween.
When Abed says that Shirley would have been ovulating over Halloween and could have conceived, Troy perks up. He remembers. He remembers the voicemail he got from Senor Chang after Halloween. Britta takes this opportunity to lay into Shirley about her lifestyle choice. For a woman who preaches about good choices, Britta points out that she slept with a married man. When your ex-husband marries someone else, he is no longer yours. With Annie's lost pen still not found, Jeff goes into overdrive. He gets everyone to start ripping up the carpet and moving bookshelves, tearing the room apart. Seeing Jeff and the others go off the rails, Annie says "It's just a pen." Everyone now gangs up on Annie. Now that they've been stuck in that room violating everyone's privacy she thinks "it's just a pen?" No one will stand for that. It's time for a strip search.
The boys are one side of the study room, the girls are the other. They each stand in front of a table they have flipped onto its side. Pierce sits in his wheelchair next to the boys' table; he's also in his underwear. After exhausting what they all thought were the possible hiding places for the pen, they realize there is one more spot the pen could have gone - Pierce's cast. Abed, Troy and Jeff run out from behind the table in their underwear and cut off Pierce's leg casts. To everyone's disappointment, they don't find the pen.
After what they've been through, Jeff realizes that anything is possible. In fact, something impossible seems more likely than possible when it comes to this missing pen. So, Jeff suggests that a ghost took the pen. Troy reminds everyone that he suggested that hours ago. After agreeing that a ghost took the pen, they all leave the study room. Once they leave, a monkey comes out of the air vent, takes a spoon and other items from the floor of the study room, runs back in to the vent and adds them to his hidden collection. In his collection are all of Annie's purple pens with the gel grip. Mystery is solved. The monkey took the pen. But, the study group will always think it's a ghost.
Dean Pelton emcees the puppy parade in the quad. The puppy floats range from political messages to purely adorable.