Monster Fink (Issue #1)
The issue begins with Sulley looking at a new advertisement made by Fungus for the company and it's new laugh energy initiatives and Mike hitting the top of the day's Top Scarers list. George accuses him of stealing props from other monsters, including himself, in order to get a high score. Mike denies any involvement in thievery and asks Sulley about a raise and maybe coming to dinner with him and Celia that night, but Sulley has been worn down by paperwork. Thinking of a way to cheer Sulley up, Mike brings Boo back into the Monster World and asks Sulley to meet him in the locker room. After a quick reunion, Mike's locker door is opened and props belonging to other monsters spill out. Boo nearly overloads the system from laughter and Sulley gets suspicious of Mike and while Mike takes Boo back to the door, Sulley makes a call to the CDA. Mike is arrested, which Sulley didn't intend, having only wanted an investigation into the matter.
Earning Celia's anger, Sulley looks into the security footage of the locker rooms and finds signs that Randall has returned and framed Mike. Randall then comes in and attacks Waxford, who's manning the cams, and plans to pin assault charges on Sulley. Sulley and Randall fight through the building and make their way to the Laugh Floor. In order to expose Randall, Sulley pulls the fire alarm and the water makes him visible. Randall is arrested and Mike is set free. Sulley apologizes for what happens, though Mike thinks Sulley did it just to lure Randall out and the issue concludes with another visit to Boo.
Fear Factory (Issue #2)
When kids are becoming too frightened to laugh for energy collection, Mike and Sulley investigate possible causes. Roz informs them that Waternoose has escaped from prison, leaving him as a prime suspect, with evading the CDA leading them to think he could be hiding in the factory and using the doors in secret. They devise a plan to set Boo's door as the only one active door to try and lure Waternoose out of hiding, though Celia insists on keeping Boo safe at her workstation. When Mike accidentally triggers a trap Sulley laid out, Waternoose bursts in to "scare the child", only to find them and immediately shuts the door.
Sulley stops it from closing all the way and he and Mike discover an unfinished one-of-a-kind scarier Factory floor designed specifically to create more Fear during the old energy crisis. They also discover how Waternoose has been getting around: A prototype "Master Door", resembling a bunch of doors assembled together capable of entering any bedroom connected to the Door network. Mike is prepared to destroy the door because of the danger, but Sulley hesitates, recognizing how the Master Door tech could make collecting laugh energy more efficient. Waternoose appears to convince Sulley to a partnership, offering to teach him how the Master Door works and revolutionize the industry again. Sulley sees through him and recognizes all he wanted to do was sabotage him and a fight ensues. Waternoose escapes into the door and Sulley destroys it instead of pursuing him. The issue ends with Mike still having trouble making a kid laugh and resorting to using the malfunctioning trap after Sulley tells him there's been no sign of Waternoose since they increased security.
Toy Worry (Issue #3)
In a crossover with the Toy Story franchise, Boo is awoken from her sleep by Sid Phillips (though he is never directly named) coming through her closet carrying a duffel bag. He is on the run from the Monsters and asks if he can hide, with Boo thinking it's a game of hide-and-seek. Mike and Sulley arrive in the room to search for Sid, who has discovered the Door network and is using it to steal toys from kids, threatening the monsters ability to make kids happy as well as the safety of the Monster World in general. When they leave, Sid comes out of hiding to thank Boo, but she soon discovers that her Jessie doll has been stolen. She puts on her Monster Disguise and chases into the closet after him.
While roaming the halls of Monsters, Inc., Boo comes across CDA agents looking for Sid, though they leave just as Boo spots him dashing through the hallways. As Boo pursues Sid, Celia spots her, but ends up grabbing the tail of Mrs. Nesbitt (the company daycare lady). As Sid desperately looks for a corner to catch his breath, Boo arrives riding on the back of an unsuspecting George Sanderson. Just as she is about to tackle Sid and retrieve Jessie, Sulley grabs and scolds her, giving Sid enough time to escape towards a ventilation shaft, followed by Boo and Mike. Mike gets stuck, and Sulley is distracted by Mrs. Nesbitt recognizing Boo's disguise as "his adorable daughter". As Sid emerges from another vent, Sulley throws the costume at him, frightening Nesbitt, and succeeding in catching Sid.
Frightened at the sight of human children and fearing an infestation, Sulley tells her to evacuate the building quietly while not specifying the reasons as not to create a panic. As Mike and Sulley turn Sid into the CDA authorities, he explains why he stole the toys: After seeing the sight of toys coming to life and attacking him during the climax of Toy Story, he decided it was best to save other kids from them, as well as making a few bucks off of selling rare ones. The monsters don't believe his ridiculous story of living toys and send him back through his sister's door. As Mike and Sulley take Boo back home and muse about how toys coming to life would be quite a story, the last panel of the issue has Jessie winking.
The final issue brings all three villains together. At a CDA briefing, it's reported that Sid has begun using door technology again and he has broken Randall out of prison. Roz suspects the involvement of the still-at-large Waternoose and that a plan for revenge on Mike and Sulley is imminent. This turns out to be the case when Sulley finds himself trapped in their hideout when leaving Boo's room after a visit, with Boo having snuck in on Sulley's back again. Mike and Celia are also there, having been grabbed by the villains earlier.
While the villains scheme on how to enact their revenge (though Sid is more interested in getting paid with the plans for door technology to get rich in the human world), the monsters try to make Boo laugh to reactivate the door and make their escape. The villains overhear them and come in to try and prevent an escape, but Boo laughs at the sight of Mike and Sulley held upside-down by their legs and her door is activated. Celia makes a mad dash through to get Boo to safety and the villains pursue them. Running through the neighborhood to find another active door, they evade Randall and Waternoose before trampolining through a window into a kid's room and waking him up. Sid comes in through the open window and manages to subdue Celia, but her hair snakes bite her in the nose and give her and Boo enough time to enter the door. When the three villains go into the door after them, they find that the CDA have already arrived. Mike and Sulley are rescued, Waternoose and Randall are sent back to jail and Sid is again returned to the human world with the hopes that he's had enough of monsters. The story ends with Mike being assigned the bedroom of the frightened kid who saw the chase, now keeping a baseball bat in bed with him, and getting attacked.