Milo faces down a cosmic storm made of negative probability ions, while Melissa, Zack, Cavendish, Dakota, Perry, and Doof work their way through the alien populace to save their friend.
Continuing from where the previous episode left off, Milo and the gang, now joined by a revived Cavendish, Agent P, and the "Cavenpus", arrive at the grounded UFO; only for Milo to once again be abducted by the same aliens.
After the school football field is ruined, an event that was meant to be there gets transferred to an old dilapidated park, where Melissa and Amanda compete over who can fix it up faster. Meanwhile, Dakota and Doof deal with an alien device that turns bones into a noodle-like substance.
Milo, Melissa, Zack, Mort, Bradley, and Amanda get in trouble with a substitute teacher and get detention. Meanwhile, the killer cyborg bear from "Now I Am a Murphy" returns to track down Milo and get revenge on him.
Zack and Milo join Melissa's athletically minded wrestling, speech, and debate team.
Six-year-olds Milo and Melissa meet for the first time, and Murphy's Law makes their first day of 1st grade a big adventure. Meanwhile, Dakota relates to Doof how he first met Cavendish while training to become time agents.
Milo, Zack, and Melissa attend a camp to learn new skills. Elsewhere, Cavendish mistakenly unleashes a giant alien.
Milo and Elliot accidentally get handcuffed together. Meanwhile, Zack and Melissa attempt to make a student film, but Doof messes everything up.
Milo attempts to escape his room so he can go out for the day with Zack and Melissa. Elsewhere, Dakota teams up with Doof to find Cavendish, who's attempting to show various news outlets a crashed U.F.O. with a malfunctioning cloaking device.
While attending a school award ceremony, Milo attempts to get to the stage in time to collect an award he was nominated for. Meanwhile, Diogee ends up riding along with two of Danville's police officers while they attempt to catch Zippy, the world's fastest koala, and rescue one of their K-9 officers.
Doof becomes inspired to find an "adventure buddy" to get over Agent P, and winds up joining Scott on a boat ride through the sewers.
After being told to go home again, Diogee crosses paths with Agent P and enemy agents after he swallows a flash drive disguised as a cookie. Meanwhile, Brigette makes Doof and Sara pick up dirty clothes, so the former builds a robot hamper-inator to do the job for them.
Eons in the future, an elderly man tells his grandson how a sentient crockpot of goulash came to be and defeated an army of robot screech owls. Back in the past, Milo, his friends, and Doof attempt to protect Brigette's goulash from Murphy's Law and Doof's hand-held-inators.
Milo gets abducted by the recurring alien characters introduced this season, while Melissa, Zack, and Doof attempt to look for him. While on trash duty, Cavendish sees the abduction from a distance, but Dakota does not. This causes a large argument between them, which ultimately ends in the dissolution of their partnership and the former going rogue.
While waiting for Milo to come join them for lunch, Melissa, Zack, Bradley, Mort, Chad, and Sara present "Neil From the Comic Shop" with differing theories on what Milo really is; ranging from him being a wizard, a supervillain, and a robot.
After discovering a boombox in the attic, Milo, Martin, and Grandpa Murphy go camping so Milo can undergo a family rite of passage to become a "Murphy Man". While the men are away, the Murphy women and Doof go to an art museum to celebrate the day without Murphy's Law, but Doof causes chaos in its place.
Elliott gets hurt because of a Murphy's Law related incident, so Milo helps him with his second job as a dog walker. Meanwhile, Cavendish and Dakota discover an alien anti-gravity device and try to show it to Mr. Block for a promotion.
While heading to a mentor program she doesn't want to be a part of, Melissa ends up paired with Savannah on a mission to stop a rampaging robot that Milo and Zack accidentally built at the science fair before it destroys half of Danville.
When his Uncle Cornelius asks for help on his farm, Zack seeks out to prove to a doubtful Milo and Melissa that a "city boy" like him can handle the job. Meanwhile, on a nearby farm, Cavendish and Dakota are assigned to pick up a fallen UFO piece from a farmer who wants to become famous in the tabloids.
While Milo is sick, two shapeshifting aliens attempt to get a tissue sample. Meanwhile, under Monogram's orders, Agent P continues to keep Doof from doing harm while attempting to do good.
Doof shadows Milo to see how he navigates around Murphy's Law. Meanwhile, Cavendish joins an extraterrestrial conspiracy support group.
Amanda helps Milo, Zack, Melissa, and Mort prepare for an afternoon concert while aliens try to covertly study Milo. Elsewhere, Cavendish and Dakota find themselves losing time and not remembering why.
Milo and his friends try to save the old clock at City Hall that Melissa's great-grandmother designed. Meanwhile, Doof tries to help the city by removing sidewalk gum under Agent P's supervision.
Sara starts to go insane from Dr. Doofenshmirtz constantly invading her personal space, so he goes out with the rest of the Murphy family to try new things
Hollywood is rebooting the first Krillhunter movie with all women, so Milo and the gang help Tobias Trollhammer audition as a woman. Meanwhile, Cavendish and Dakota try to catch an alien while picking up trash by the highway.
Milo and Amanda get the chance to be on the latter's favorite TV show, Cake 'Splosion!, an extreme kids' cooking show.
Milo and Elliot are the pace car drivers for a charity race.
Milo and his friends and family decide to finally attempt to finish a board game.
Doofenshmirtz reminisces on an adventure he had with Diogee the previous summer after the canine got caught up in an Agent P style mission.
After Scott the Undergrounder and Mrs. Murawski appear to hit it off and set up a date, Milo and the gang attempt to help the former look more presentable and normal.
Milo, Zack, and Melissa—with help from Phineas, Ferb, Candace, Buford, and Baljeet—help conquer Murphy's law to stop a swarm of Pistachions.
Milo Murphy is the personification of Murphy’s Law where anything that can go wrong will go wrong. Suffering from Extreme Hereditary Murphy’s Law condition (EHML), Milo always looks to make the best of the cards he’s been dealt and his endless optimism and enthusiasm can turn any catastrophe into a wild adventure. Together, he and his friends will learn that it’s all about a positive attitude and not to sweat the big stuff… and it’s all big stuff.