• In Comet Observatory, Rosalina tries to put the Lumas to bed with stories of Peach and then Mario, but is interrupted by Bowser Jr in a giant robot. Rosalina makes quick work of it at first, but Bowser Jr takes a cheap shot at a nearby Luma forcing Rosalina to lower her defenses an get captured along with the Luma.
• Mario and Luigi drive dirt bikes to a desert town of near inverted pyramids to help out with a troublesome pipe. Using the fire flower powerup, they enter and find a pipe full of rubble. They clear it to find Yoshi who immediately becomes friends to them them. Through a flashback, we find out Yoshi had apparently been stuck in New York for a bit before being chased onto the pipe.
• Bowser Jr is holding Rosalina and the Luma for purposes unknown, but when the Luma is hurt, Rosalina does enough damage to allow it to escape while she is recaptured. Bowser Jr will somehow use her in a plan to rescue his father.
• Mario, Luigi, and Yoshi prepare for Princess Peach's birthday party, with Yoshi and Luigi making fun of Mario's crush on her.
• They all go to the castle and Toad is not enthused to see a new member of the group, Yoshi. Anyway, Peach is not at her own party, but hanging out on the roof of the castle watching fireworks. Mario appraches and she laments not knowing where she's from or what her real birthday is. Mario cheers her up with a present, a pink parasol. Then, strange star bits start falling to the sky, followed by a large meteor crashing a ways out beyond the castle.
• They find it is the escaped Luma who came to Peach for help because Rosalina said they could count on Peach if something happened. The toad advisors and Mario overhear, with the toads insisting she can't go, but Mario makes them leave her alone to consider.
• Peach decides to help and takes Toad (the main toad) with her. The Luma transforms into a Launch Star and the two quickly leave the planet traveling a series of Launch Stars.
• The next morning, the princess is discovered missing and they give Mario the note left for him. Peach instructs him to take care of the Mushroom Kingdom.
• In a montage, Mario, Luigi, and Yoshi travel about the kingdom stopping enemies and fixing things. Doing good work, but tiring themselves out.
• Mario and Luigi check in on the shrunken Bowser, who has taken up painting and has a good relationship with Luigi now. Mario doesn't trust him and Bowser gets angry. Still, Bowser seems to have a better rein on his anger. Bowser Jr's sauser ship arrives and begins trying to take the castle using a tractor beam. Mario and crew get all the toads out, but find themselves in space aboard the castle.
• Bowser Jr arrives and a huge fight in the castle occurs, with Bowser Jr's magic paintbrush allowing him to overpower Mario, Luigi, and Yoshi. Yoshi manages to take control of the robot and eventually destroys the tractor beam, causing the castle to fall out of space onto a planet of giant flowers. The crew is almost killed by the falling debris of the crumbling castle. Mini Bowser tries to escape, but is captured again. When informed of Bowser Jr's arrival, Bowser suddenly becomes reflective, thinking his son must hate him.
• Peach and Toad arrive at the transport galaxy, a hub world where they can find a pilot to anywhere else. Peach sees a Missing Rosalina poster and has a flashback. She's seen her before somehow, as a baby. Then a monkey scams them and steals Toad's supplies. They chase it down and corner it but it jumps through a glitch in a wall. Peach and Toad carefully follow, finding themselves in a seedy bar full of enemy koopas and goombas.
• Mario and crew continue across the flower planet, with Bowser begging to be be made big again so his son will have someone to look up to. Mario refuses, but Bowser goads him into hitting him, causing the Mini Mushroom powerup to be lost, and Bowser becomes big again. Bowser really does seem to have changed, however, and peacefully joins their party, as they spot a castle in the distance.
• Peach and Toad continue the chase on what turns out to be the inside of the planet, which is a cube with weird gravity and covered on all six sides with a casino. The monkey brings the stolen goods to the leader who turns out to be Wart from Super Mario Bros 2. All the other Mario 2 bosses are there. Wart makes a comments that princesses keep getting captured. Peach demands to know what he knows about Rosalina. Wart threatens her, so she and Toad defeat all the bosses of Mario 2 plus hundreds of Ninji (yep, overpowered) before forcing the info out of Wart. They leave with Toads supplies, but Wart angrily contacts Bowser Jr to tell him about Peach.
• The Mario crew arrives at the castle of the Queen Bee where Bowser is forced to stay outside. Mario asks for help getting off the planet, but the queen insists he be imprisoned for destroying her flowers with a castle. Bowser nobly volunteers to be emprisoned on their behalf so they can leave and the Queen agrees. Mario is impressed with Bowser. The Mario crew leave him and take a giant flying bug as transport off the planet.
• Bowser is shown breaking rocks in a prison work crew, lamenting how he lost his first love (Peach). Suddenly, Bowser Jr's tractor beam takes him and they have a reunion. Bowser is awestruck at what his sone was able to build.
• Bower Jr reveals his motivation, and how much his dad means to him by recounting the puppet shows Bowser used to do for him. We are shown, in puppet form, Bowser's old plan to rule and/or destroy the universe. It involved building a planet for his forces and a doomsday weapon to destroy anyone who got in their way or made fun of them. Bowser Jr has been working on this plan in Bowser's stead for years.
• Returning to Peach and Toad, they return to the front side of the planet and as ROB the robot for directions to the space port. ROB glitches out while doing so. When they finally make it, no pilot wants to take them where they want to go. Far too dangerous. Fox appears, having overheard their quest. Doing a quick and humorous introduction, he agrees to transport them for the right price. Toad shows off the gold coins and the deal is struck.
• Mario and crew, en route, discuss Mario asking Peach out, and then Luigi asks Mario to find out if Peach has any friends for him to date. After landing, they too encounter ROB the robot and are directed (with some glitching) to the princess.
• At the space dock, all our heroes are reunited, though Toad is as unenthusiastic about Yoshi as ever. Mario awkwardly tries go give Princess Peach a handshake instead of a hug while Luigi facepalms. Fox is introduced to them and they all board the Arwing and fly into space.
• Almost immediately, they are attacked by Bowser Jr's saucer. Fox makes quick work of its automated defenses with the plasma canons on the Arwing. Bowser Jr goes to a weapon cabinet to get a giant bazooka to shoot them down. Bowser, still caring for the Mario brothers, asks if they might avoid killing them. Bowser Jr thinks this is strange but grants his father's request, using a SNES Super Scope weapon. This weapon hits Mario and Luigi on the Arwing, turning them into their baby selves. Messing with the Arwing, the ship starts to crash, as Bowser yells in distress. Bowser Jr drops the weapon to return to his plan while Bowser looks conflicted.
• Fox and crew crash on a jungle planet. They're safe, but the Arwing is damaged heavily. The babies wander off. Yoshi and Toad go after them and find the babies messing with a sleeping T-Rex. Toad manages to get them away, but Yoshi, having found the Super Scope weapon in a tree, makes too much noise and wakes the T-Rex. They are chased through the jungle where Yoshi uses his tongue like Spiderman's webshooters. Toad is accidentally transformed into a baby as well, and Yoshi tries to get them all to safety. Falling off a bridge into a lake, the T-Rex almost eats Yoshi before being turned into a baby itself by the Mario brothers messing with the weapon. They revert everyone but the T-Rex back to adults.
• Back at the ship, Fox freaks out at the damage to his ship, while Peach has a small tantrum at her inability to do anything. Mario comforts her. Luigi, messing around, sends out a distress signal on the Arwing's radio, which the Lumas in the Comet Observatory pick up.
• Bowser laments losing his friends, and Bowser Jr says this is a good thing because friends can never be trusted, only family. Using Bowser's own teachings from the past, Bowser Jr tries to convince Bowser to return to his old ways before saying he has a surprise to show him.
• The Lumas bring the Comet Observatory to the jungle planet for a rescue. Peach finds the storybook Rosalina tried to read to the Lumas at the beginning of the film. It reveals that Rosalina and Peach were sisters, made of stardust. They had a power together, but that caused them to be hunted, so Rosalina sent her through a pipe to be raised in the Mushroom Kingdom.
• Bowser Jr introduces Bowser's dream made reality: Planet Bowser is built, and has a fully functional doomsday weapon. He shows how he is using Pricesss Rosalina as its power source. Bowser Jr tells his dad to return to his true self and Bowser relents, becoming the King of the Koopas once again. The weapon starts to power up and begins sucking energy from Rosalina trapped in the machine.
• Fox is excited to fly this new ship and they all load up, with the Lumas becoming big fans of Fox in the process. Jetting off, they attack the unsuspecting Bowser fleet and destroy many ships. Fox creates an opening for the rest of the crew to do a covert Launch Star insertion onto Planet Bowser. Fox flies off to distract the rest of the fleet.
• Mario, Peach, Luigi, Yoshi, and Toad land and begin sneaking around. They split up with Mario and Peach going one way and the rest another way. The Luigi group find a cache of powerups. Mario and Peach, however, are spotted.
• Bowser Jr is alerted to Mario's presence and he decides to use his "security system" on them. After causing them to fall into a trap, Mario and Peach find themselves inside what is essentially a Mario Maker level from hell. Mario and Peach show real symmetry, helping each other through the various traps and completely defeating the trap, much to Bowser Jr's surprise. Bowser assures his son that he'll take care of them.
• Mario and Peach are confronted on a metal bridge above a lava pool. Bowser is very angry and beyond reason. Mario tries to reason with him, but it's no good. Regretfully, Mario uses an ax to cut the bridge while Bowser is on it, causing him to fall into the lava. Bowser Jr is heartbroken and cries for his father. Mario and Peach feel sad for him. Then, a claw reaches out of the lava. Bowser has become Dry Bowser, made of bones. His dip in the lava changed his body, but his mind is exactly the same. Mario forces Peach to go on without him as he faces down the Bowser duo.
• Peach reaches the massive machine siphoning energy from Rosalina.
• Mario fights the Bowsers but he's not doing so hot. Yoshi and Luigi appear with powerups and the tide of battle quickly turns. In the huge fight, Luigi gets his hands on Bowser Jr's magic brush and tries to draw something. This becomes a Mr. Game & Watch. No-one is impressed, but the Mr. Game & Watch uses his judge hammer to one-shot destroy Dry Bowser, shooting bones everywhere. Bowser Jr becomes livid and uses his ink to create the Ruined Dragon from Mario Odyssey. The dragon, however, immediately turns on Bowser Jr and eats him whole. Mario uses the Flying Mario powerup and kicks a hole straight through the dragon, destroying it and saving Bowser Jr. With that, the battle is effectively over. Bowser Jr reunites with Bowser but they are otherwise no longer a threat.
• Peach scrambles her way to the center of the machine holding Rosalina, who is fading away quickly as the weapon continues powering up. Unable to break into the cell, Peach gets Rosalina to join her hand so their power can resonate. This works and the machine is blasted apart, with the weapon powering down.
• With the princess sisters reunited, Peach introduces her sister to Mario. Fox brings the Comet Observatory back and all the Lumas reunite with Rosalina. They beg to go see the castle in the Mushroom Kingdom.
• Cut to the hole in the ground where the castle used to be and everyone is looking expectantly to the Mario brothers. Mario suggests they build a new one, and the Lumas are happy to help out.
• After a building montage, Peach gives Mario a kiss and he uses the cape to fly up and christen the castle with the flag on the highest spire.
• Animated Puppet Show Credits!
• First post-credit scene: Fox mentions to a toad that Rosalina fixed up his Arwing and now he's headed home. Then we see Bowser (as a pile of bones) encouraging his son as he attempts to dig his way out of the prison cell. The crazy blue Luma from the first film reveals himself as the prison guard, scaring and tormenting them while telling Bowser that soon, his bones will turn to dust. Bowser and son scream.
• Actual Credits!
• Second post-credit scene: In the space port, the monkey from before tries to scam and then steal from another person. The monkey is quickly punched from off screen by a gloved hand. The person thanks his savior, who is revealed to be Princess Daisy.

The first one is after the animated credits showing the main actors. It has Fox talking to a Toad, saying he got help from Rosalina to fix up his warp drive and will now be able to get back to Lylat. Then, it shows Bowser Jr and Bowser in a jail cell planning an escape, only to be psycologically tormented by the insane blue Luma from the first film.

After the rest of the credits, the final post-credit scene shows the monkey from earlier in the film steals another character's bag, only to be punched by a gloved hand. This turns out to be Daisy. Cut to black.

It's really hard to see, but in Fox's cockpit, barely visible, there's a photo of Krystal on taped to one of the panels. She's wearing a flight jacket instead of her Adventures or Assault clothing. There's one lipstick kiss mark on the corner too.