During Mario and Luigi's infancies, the Mushroom Kingdom is facing against with one of its greatest trials: the Shroob invasion. On a distant planet shaped and colored like a Poison Mushroom without eyes, there lives a vile and evil race of aliens known as the Shroobs. They begin searching for a planet worthy of invasion. They ultimately find the Mushroom World, specifically the Mushroom Kingdom. Plans for an attack are presumably soon under way.
Baby Bowser just so happens to pick the same day that the Shroobs invade the Mushroom Kingdom to kidnap Baby Peach. Attacking the main castle, Baby Bowser battles Baby Mario, accompanying with his little brother Baby Luigi to play with Baby Peach, and is quickly defeated. However, this allows the Shroobs to catch the distracted Toad guards, who were unaware of their invasion. Everyone winds up being forced to flee. Young Toadsworth, Baby Bowser, Baby Mario, Baby Luigi, and Baby Peach, in her carriage, follow Baby Bowser's assistant, Kamek, to the Koopa Cruiser, which the Koopas is using to travel to his castle. They escape from Baby Peach's Castle as quickly as possible.Toadsworth promptly faints, and Toad asks Mario to get the Refreshroom that Toadsworth keeps in his room, for it can help revive him. Finding it inside a block above Toadsworth's garden, Mario brings back the item just as a Toad doctor is diagnosing it to be the only way to bring Toadsworth back. Mario uses it on Toadsworth, who comes to in time to see the return of the time machine from his hospital bed. The time machine is in a worse state than when it had left. When it is being approached, a large alien comes out. Mario takes the alien down while everyone is gathering around after Toad reappears from entering the capsule who announces that the princess was not inside the time machine. E. Gadd is at a loss as to what is happening. After all, he had been more than 99% sure that Princess Peach would return all right after her return from the past.With many years passing, adult Mario and Luigi watch with rapt attention asProfessor E. Gadd reveals his latest invention: the time machine. It is such an important occasion that a Lakitu is on hand, broadcasting it onto live television. E. Gadd reveals that his machine runs on the power of the mysterious Cobalt Star. Adult Princess Peach is so overjoyed by the invention that she asks the professor to take it for a spin. Toadiko and Toadbert accompany the princess on her journey. Despite Toadsworth's pleas, the three travel back in time to a younger Mushroom Kingdom, when the princess and the Mario Bros. were mere youngsters.
Luigi soon discovers a mysterious new hole out in the courtyard. E. Gadd elaborates that it is a time hole, or a rip in the spacetime continuum. It is caused by the use of the time machine that he had invented. Luigi goes closer to investigate, standing on the raised edge of the hole. Suddenly, Toadsworth panics. Rocketing into the courtyard, still on his hospital bed, he crashes into the hole while demanding answers. However, this causes Luigi to lose his balance and fall into the hole. Mario jumps in after his brother to rescue him.
When Mario pops out of the time hole, he finds himself in a strange land near Hollijolli Village (standing on top of Luigi). Suddenly, after Mario jumps off Luigi, a suitcase pops out of the hole and also lands on Luigi. Stuffwell, E. Gadd's seemingly sentient suitcase invention designed to assist time travelers, informs Mario that he was there to help out. Stuffwell explains to the two brothers how to fight, jump, and learn other techniques on their journey afterward.
Back in the past and shortly after the babies' escape, a time machine appears in the castle throne room. A fully grown Princess Peach and her loyal assistants, Toadiko and Toadbert step out. The Shroobs suddenly stop their invasion and let their leaders, the Elder Princess Shroob and Princess Shroob confront Peach. Thinking fast, Princess Peach grabs the Cobalt Star from its place in the time machine. As the younger Shroob princess watches, Princess Peach holds it above her head, and forces the star to consume the Elder Princess Shroob inside of the star, then shattering it into six pieces. However, the other Shroob princess is able to capture Princess Peach, while Toadiko and Toadbert run away.Although the Shroobs had lost their leader, Princess Shroob (the second in command) takes command of the Shroobs and their operations and they still begin their conquest of the entire Mushroom Kingdom. Toad Town falls as the Shroobs swarm from Princess Peach's Castle. In a short period of time, the Mushroom Kingdom falls under complete Shroob control.
Meanwhile, time holes begin appearing all over the Mushroom Kingdom. One such hole appears just outside of Hollijolli Village. Shortly afterward, a grown up Mario and Luigi pop out of it. Stuffwell follows, after which the time hole disappears. Arriving in the village, they find it devastated from the Shroob attack. After they find the mayor, the Shroobs arrive again, abducting the mayor, and proceed to battle Mario and Luigi. The Shroobs prove to be too powerful for Mario and Luigi to defeat alone. However, in the Koopa Cruiser, Baby Peach is crying because Baby Bowser does not want to stop helping the poor people attacked. Baby Bowser, wanting to save his ears, destroys the Shroob UFOs around Hollijolli Village; the baby brothers then proceed to fight the Shroobs who battled the adult brothers and are able to defeat them. Afterward, Mario and Luigi are brought aboard, where Toadsworth disregards their story, thinking that they were not right in the head. The heroes, both past and present, then witness what has happened to Peach's Castle. It has been turned into Shroob Castle, with a giant Princess Shroob statue in the center.
Later, a group of Shroobs begin attacking the Koopa Cruiser. Baby Bowser informs his pilots to launch the Koopa Cannon to shoot them. Suddenly, a figure appears above the Koopa Cruiser. It is Princess Shroob, who launches a missile at them, taking down their engine. They crash land into Bowser's Castle. Mario and Luigi, the only ones other than Stuffwell who have not been thrown clear by the crash, began to make their way through the castle, informed by Stuffwell that there was a time hole nearby. They find Baby Mario and Baby Luigi on the way. Once Stuffwell explains to them how to control a group of four, the babies travel with the older brothers. After they find a mysterious sparkling shard, they, in addition to Baby Peach and Toadsworth the Younger, all travel through a time hole in Baby Bowser's room that leads back to the present day Princess Peach's Castle.Once back at the present castle, Stuffwell shows Professor E. Gadd the mysterious shard, which the professor identifies as being a shard of the Cobalt Star, the power source of the time machine. The Cobalt Shard then flies over to the defeated Junior Shrooboid, who then reacts to the Cobalt Shard. The Cobalt Shard afterwards creates another time hole, and E. Gadd sends Mario, Luigi, Baby Mario, and Baby Luigi to investigate. As they all enter the time hole, Toadsworth is chasing Toadsworth the Younger, who has Baby Peach in his arms.
After the heroes enter the time hole, they find themselves at Toadwood Forest. Later, they discover Toadiko, who is wrapped in a tree's branches. She gives them some information as to what happened to her, Toadbert, and Princess Peach (although she had not explained the full details), then tells them that there is a Cobalt Shard at the Vim Factory, where vim that is sucked out of Toads bound to the forest trees is used to make fuel for Shroob UFOs. Shroob UFOs then attack, and Mario and the gang run, while Toadiko is transformed into a Shroob Mushroom.After Mario and gang reach the Vim Factory, the L33t Hamm3r Broz. use a suction-type tree and capture Mario and Luigi, leaving the babies behind. The Hamm3r Broz. challenge the babies to a battle. As usual, the babies win and the helmets on theHammer Bros. break, freeing both Hammer Bros. from the Shroob's control. They give the babies Hammers and teach them how to use them. The babies travel through the air shaft and finally rescue Mario and Luigi. The babies continue moving along, with their older selves, towards the rest of the Vim Factory.
In the last room, they find a huge Shroobified Wiggler named Swiggler. Mario and Luigi watch Swiggler give the Shroob UFOs energy, but Baby Mario knocks the vim holder. This enrages Swiggler, causing it to battle. When the boss is defeated, another Cobalt Shard is found. However, Baby Bowser comes in, running around the four heroes. As a result, Mario, Luigi, and the babies become dizzy and Baby Bowser is able to steal both Cobalt Shards. Baby Bowser and Kamek escape, and the heroes travel back to the present day Princess Peach's Castle, both successful and unsuccessful.
When they return to the castle, Stuffwell informs the professor of their dilemma. He tells them that time holes have been popping up excessively and that they should find Baby Bowser, along with his stolen Cobalt Shards, in one of them. E. Gadd then tells them that some young fellow and Toadsworth have been squabbling and that the brothers should investigate. In the courtyard, Toadsworth and Toadsworth the Younger are trying to cheer up a crying Baby Peach. They do so by spinning on each other's head. Luigi is impressed by this move and wants them to teach it to him, along with his older brother, Mario. After they learn the Spin Jump technique, the brothers use it to reach the only available time hole, which is located in the second floor library. Using their new Spin Jump move, they reach the time hole, taking them to the Yoshi's Island of the past.
On the island, they notice that all of the Yoshis have disappeared and a giant, purple and green egg shell is left. They enter one of the huts where they run into Kylie Koopa, who is a reporter looking for the scoop on the mysterious egg. The babies use a spring to find all of the Yoshis hiding in the attic. They are hiding from Yoob, a Shroobified Yoshi who has been eating other Yoshis. A Yoshi tries to fight Yoob, but is easily eaten like the rest. Kylie tries to take some pictures of the scene, but gets swallowed doing so. She is then spit out, and is shot into the hut that the brothers are hiding in. After Yoob leaves, the brothers find Kamek facing off against the giant Shroob monster. Like Kylie, he is eaten, then spit out. Before he leaves, Kamek mutters something about needing to get Bowser a snack. The heroes then enter a hut which leads to another part of the island as they discover Yoshi Cookies. Mario leaves them alone, but Luigi decides to take them with him. He almost eats one, but then decides to give it to Baby Luigi.
As the plumbers continue through Yoshi's Island, they spot Kamek again. Mario and Luigi try to get him, but he escapes and tries to burn the island in order to keep them busy. Stuffwell then learns that they can use Baby Mario's ability to spit water, extinguishing the flames. The adult and baby brothers used their newly learned abilities to pass through the puzzles off the island and make it to the top of the cliff, where Prince Bowser is eating all of the Yoshi Cookies from the island. While Kamek tells him to slow down, Mario and Luigi confront them as Baby Mario and Baby Luigi start eating the Yoshi Cookies. In their discussion, Prince Bowser says that he is going to keep both the Cobalt Shards because Mario previously stole one of the Cobalt Shards from him and the other will be consolation. He also intended on keeping all of the Yoshi Cookies, but the baby brothers ate them all. As a result, Prince Bowser goes into a tantrum. Kamek says that he would take care of it as he fights the brothers. Kamek uses his magic to duplicate himself, create fire, and power himself up. He is ultimately defeated, however, as the brothers chase after Prince Bowser. The prince reaches a dead end, and as a last resort, eats the Cobalt Shards, finding them to be interestingly delicious. As Mario and the gang try to get the Cobalt Shards out of Prince Bowser, Yoob climbs up the cliff and is shot by a ray from a Shroob UFO. The ray causes him to grow incredibly large, and he devours Mario, Luigi, Baby Mario, Baby Luigi, and Baby Bowser.Inside Yoob, the brothers and their smaller counterparts find themselves in the intestines of the creature. They rocket themselves into the stomach, where they find a Yoshi trapped. It is trying to push a big Chomp Rock to make more space in Yoob's intestines and find an escape route. However, the rock is far too heavy for the dinosaur to push alone, and the four heroes wander throughout Yoob's Belly and enlist the aid of several other swallowed Yoshis to help push the Chomp Rock. Luckily, there are enough Yoshis to push the Chomp Rock, and as a result, everyone could travel through more of Yoob's Belly. Mario, Luigi, and the babies battle their way through the monster's intestines, encountering Dry Bones and RC Shroobers on their way.
Later on through the digestive process, they discover that there was a factory inside Yoob, turning Yoshis into strange eggs for unknown purposes. Fortunately, the babies manage to shut down the factory. Toadbert is first seen here, having apparently lost his memory. The only thing that he could remember is a strange drawing that he himself made but does not recall what it meant. He decides to give it to the brothers, not knowing what they could do with it. Farther on, they discover the mastermind behind the egg factory: a giant egg like monster called Sunnycide and afterward, it throws an egg at the brothers, which happens to contain Prince Bowser. Freeing the Yoshis and enlisting their help, the brothers defeat Sunnycide. After that, they escap from Yoob out of the end. Prince Bowser coughs up the Cobalt Shards, and the brothers grab them and run.
Back at the castle, the adult brothers once again learn a new move from the Toadsworths, Bros. Ball Using this move, the brothers could curl themselves into a ball to roll around. Using this new power, the brothers solve a puzzle allowing them to access the highest area of the castle where the next time hole is located. This particular time hole takes them into the middle of the Gritzy Desert. A huge colosseum is located in front of them. Mario and the gang try to get in, but are quickly chased away by the Shroobs that are inside. They run away and hide behind a pillar. The babies walk away and Luigi will stop them, but they get caugh and run away, while Kylie Koopa appears again and informs Mario, who left behind, about the four pillars of the desert, saying that they have some mystical connection that could help them. By telling, a hilarious spectacle plays with Luigi, the babies and a Shroob chasing each other. The older brothers and baby brothers then separate and activate the huge pillars, all of which resemble Dry Bones. Suddenly, beams of light shoot out of each statue's eyes, connecting with each other. The connection causes a secret entrance to the Koopaseum to be open. The brothers then sneak into the arena.Within the arena, Princess Shroob is hosting a celebration about the conquest of the Mushroom Kingdom. Princess Peach is revealed, being strapped to a platform. The platform is lowered towards a large Warp Pipe. Petey Piranha is in the Warp Pipe, jumps, and eats the princess. The brothers stand in shock, unaware that Kylie Koopa is just taken away by Shroobs. The brothers sneak through the Koopaseum in search of Petey, but unfortunately, they accidentally end up onstage, where Princess Shroob is still standing. She calls upon the Shrooboid Brat, who attacks the brothers and entertains the crowd at the same time. The brothers, however, defeat the brat, angering Princess Shroob. With the assistance of her lackeys, she breaks the floor under them, sending them to the caverns below.
In the Gritzy Caves, the adult brothers are knocked unconscious by the fall. Baby Mario then hit Luigi with his Hammer, which awakens him and he scares the babies, who start to cry. Mario is awoken by the babies crying and confronts Luigi. They then decide to not turn on themselves and continue through the caverns, where they are constantly attacked by Dark Boos, Snifaros, Elite Boom Guys and Bob-ombs. After a while, they see Kylie Koopa tied by a rope, hanging down towards Petey Piranha's open mouth. Some Shroobs are also there, ready to begin the execution. Kylie pleads for the brothers to rescue her, saying that she is the one who told them about the secret entrance. Unfortunately, Mario and Luigi could not reach her, so they could do nothing but watch in horror as one of the Shroobs grab an axe from its body and cut the rope. Kylie Koopa, still tied by rope, is eaten by Petey Piranha. The brothers have no choice but to continue.
After hitting a block a couple of rooms later, the heroes are attacked by Petey Piranha, whom they battle and, after a struggle, defeat. Another Cobalt Shard pops out of the plant, along with Kylie Koopa, surprisingly free of the rope, who finds a key in the plant's belly. While talking to Kylie, she tells the brothers that she saw someone in the Cobalt Shard. However, she and the brothers think of that as being very unlikely, and continue their adventure.A little farther, the brothers enter a cell, where the find Princess Peach, whose face is covered by a Shroob Mushroom. She and Luigi, who is horrified by her appearance, both collapse and are taken back to the present day castle. Everyone gathers in the room of the Princess, where they discuss the Princess and the Shroob Mushroom. Princess Peach then decides to take a nap and the brothers are shoved out of the room.
Downstairs, Mario and Luigi are taught yet another move by the Toadsworths, Baby Cakes, where the older brothers could flatten the babies using their Bros. Ball technique. During the lesson, the Toadsworths flatten Baby Princess Peach, who is swept away by a gust of wind. The four heroes use their new moves to save her. Mario and the gang then leave the Toadsworths, where they meet some panicking Toads. Curiously, the heroes travel up the castle to see Princess Peach. It turns out that Bowser is just about to kidnap her, and he runs through the castle with the princess on his shoulder. However, Bowser falls through the floor and lands in the next time hole.
The brothers went into the time hole that Bowser was in and wind up at Thwomp Volcano, which they climb to the top of, battling various enemies, such as the block shapedThwacks. At the top, they learn that the volcano is close to erupting. They then meet Professor E. Gadd’s younger self, who is panicking because the volcano is going to ruin all of his inventions. He thinks up of an idea of making a machine that could douse the volcano's fire, which the older E. Gadd creates in the present time. He then uses his quickly built invention to spray water into the time hole and stop the volcano, angering many native Thwomps. One of those Thwomps was Mrs. Thwomp, who battles the brothers but is defeated. Her husband agrees to take the brothers in the volcano, where they solve various puzzles to destroy blocks that are obstructing their path to the bottom. Then, they fight and defeat Bowser and Prince Bowser, (who was shot into the volcano after being blown away from Yoshi's Island). Before they can rescue the Princess, she is sucked up by theShroob Mother Ship. The courageous brothers followed her.
Inside the Shroob Mother Ship, the heroes fight a few Guardian Shroobs and later meet up again with Kylie Koopa, who saves them from the Shroobs and Princess Shroob disguised as Princess Peach. Kylie takes them into a room to try and solve the secret of the Shroobs with the large, mysterious key she found earlier. She inserts the key into a large machine, but it actually causes them to fall out of the ship. Kylie lands on Yoshi's Island, while the brothers end up in Toad Town, where everyone is gone except for two elderly Toads, who help them stock up on gear.In the Star Shrine, after finding the fourth Cobalt Shard, the brothers meet up with Toadbert and Kylie Koopa, who reveal how to clean Toadbert's picture, given to the brothers back in Yoob's Belly. It turns out that another Princess Shroob was on the picture. Before the drawing was explained, Mario and company are attacked by the Elder Shrooboid, who attacks Toadbert and Kylie Koopa, causing them to become Shroob Mushrooms. The four brothers fight the Elder Shrooboid. Although the Elder Shrooboid is much more powerful than the Junior Shrooboid, they are able to defeat it and the heroes acquire another piece of the Cobalt Star.After they solve some puzzles, the four brothers escape the Shroob infested Toad Town and find a Warp Pipe that takes them to Star Hill, where they are attacked by theCommander Shroob, his Support Shroobs, and a Shroob-omb. Once defeated, the four heroes head up Star Hill and the Cobalt Star creates a path so that they can get to the Star Shrine, where another Cobalt Shard is located. At that time, the spirit of the Cobalt Star began to talk to the brothers about defeating the Shroobs. Baby Luigi begins to cry afterward for a strange reason. The brothers did not know why, however, but they calm him down. They then travel to the Star Shrine, where a gate needs to determine if the heroes had pure hearts to get past it. Mario and the babies did, but Luigi did not, apparently. Mario knows that he is not going to leave his brother alone, so he and the other heroes are placed through a trial to prove that Luigi has a pure heart, finding theAurora Block. Shortly after, they get the block and gain access to the Star Shrine, where they learn that Luigi had a pure heart the whole time, and was only being tested.
They then return to the castle, where they are told to go to the Shroob Castle in the past. The brothers solve many puzzles in the large castle, and even take down the Shroob Mother Ship. Mario and the gang finally find Princess Shroob, along with Princess Peach. After a long battle, the brothers defeat the Shroob princess. Then, Princess Peach shows them the last piece of the Cobalt Star, but does not let them merge it with the other pieces that they have. Before she could explain, Prince Bowser swoops in and takes the final piece and connects it to the other pieces, causing Elder Princess Shroob to appear. He is then transformed into a Shroob Mushroom, as well. Peach finally reveals that she trapped Elder Princess Shroob inside the Cobalt Star and the final piece freed her. After that, the brothers fight the mighty Elder Princess Shroob. After beating her, she turns into a dark colored Mushroom. As the brothers try to figure out what to do with the Mushroom that was once Baby Bowser, the babies play around with it and Baby Luigi gets hurt. He begins to cry on it, which restores Baby Bowser to his true form. Realizing the Shroobs' weakness, the gang gets Professor E. Gadd to spray a chemically similar liquid to Baby Luigi's tears all throughout time with his invention, the Hydrogush 4000, causing all of the victims of the Shroobs to turn back to normal and ridding the presence of the Shroobs in the process.The brothers soon return to Peach's Castle where they find Bowser lying on the carpet, completely knocked out. As the brothers wonder what to do with the behemoth reptile, the Mushroom that is Elder Princess Shroob hovers into Bowser's mouth, who weakly eats it and turns into Shrowser, a form of Bowser in possession of Elder Princess Shroob. He is relentless, but the brothers use his attacks against him and defeat the manipulating form of Elder Princess Shroob. Afterward, Toadsworth the Younger, Baby Peach, Baby Mario and Baby Luigi all use the repaired time machine and travel back to their own time, bidding farewell to their future selves.
Playable Characters
MarioLuigi
Baby Mario
Baby Luigi
Supporting Characters
ToadsworthPeach
Baby Peach
Professor Elvin Gadd
Kylie Koopa
Princess Shroob
Baby Bowser
Young Toadsworth
Toadbert
Bowser
Toad
Yoshi
Elder Princess Shroob
Kamek
Young Elvin Gadd
Fawful
Toadiko
