While on the subway on a school field trip, Milo’s car gets thrown off course and he, Zack and Melissa discover an underground city of subterranean creatures.

Sara wants to go see The Doctor Zone Files movie with Milo, but worries about potential problems.

The other school kids, led by Melissa and Zack, throw a surprise birthday party for Milo at a go-kart arena.

Milo and his friends visit a dude ranch. While horse back riding, they meet a girl named Jackie who joins their posse, and Zack is smitten with love. But, Jackie leads them into more danger than usual. Meanwhile, Sara is going crazy because the ranch reminds her of scenes from The Doctor Zone Files, and invites other fans to join in the geek fest.

When Milo accidentally joins another family on their vacation, the new family must learn to cope with Murphy’s Law.

The gang participates in a school event that combines both the academic and athletic decathlon.

At a donation drive, Milo accidentally gives away his mother's vintage T-shirts. Meanwhile, Cavendish and Dakota are assigned to protect the pistachios at the zoo.

Amanda is concerned that Milo will ruin everything at her carefully orchestrated school dance.

Milo, Melissa, Zack, and Mort's band enters the battle of the bands, where Zack discovers his old boy band is competing.

Milo, Zack and Melissa go to school after sunset to retrieve Melissa's math book. Unfortunately, she leaves the spare key inside the locked classroom, so the three go on a "quest" in search of the mysterious janitor, otherwise known as the "key-keeper".

When Cavendish and Dakota stop Milo from destroying a pistachio plant, they change the future. Pistachio plants become sentient and take over the planet, so Cavendish, Dakota and Milo must race through time to save the future.

Elliot Decker is hired as the school’s head safety monitor.

Milo, Zack and Melissa set out in search of a missing robot that previously escaped.

Parents become children at Back to School Night.

Milo runs a race as Cavendish and Dakota gets stuck in the Old West.

With Milo away skiing, Sara finally feels safe enough to go on a date.

Dakota travels back in time to save Cavendish.

Milo surprises his parents by inviting the extended Murphy family to town for Christmas, multiplying the effects of Murphy’s Law.

Milo, Zack, and Melissa—with help from Phineas, Ferb, Candace, Buford, and Baljeet—help conquer Murphy's law to stop a swarm of Pistachions.

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.

Doofenshmirtz reminisces on an adventure he had with Diogee the previous summer after the canine got caught up in an Agent P style mission.

Milo and Elliot are the pace car drivers for a charity race.

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.

Learning that the local skating rink is closing down, Milo convinces his parents to pursue their dream of winning a disco skating competition they were unable to finish years ago before that happens. Elsewhere, Cavendish and Dakota are assigned to pick up seemingly ordinary lawn gnomes from a little old lady.

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.

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.

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.

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.

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.

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.

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.

After Zack breaks his leg getting tangled in a harp while doing interpretive dance, all of his friends plan a "cast party". At said party, everyone shares stories of how they all broke something without Milo, Martin, or Murphy's Law around; as far as they know.

Milo, Zack, and Melissa attend a camp to learn new skills. Elsewhere, Cavendish mistakenly unleashes a giant alien.

Zack and Milo join Melissa's athletically minded wrestling, speech, and debate team.

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.

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.