Princess Peach gets her voice stolen by Cackletta and her evil henchman, Fawful. The Mario Bros., of course, go to save her, along with Bowser, who wants to kidnap her. They must travel to the Beanbean Kingdom to meet Cackletta. By the Koopa Cruiser, the three characters travel to the kingdom, but are shot down by Fawful, making them land in Stardust Fields. It is later revealed that Cackletta wanted to steal Peach's voice to waken the Beanstar, a special item that must be awakened by a beautiful voice, allowing her to possibly rule the world. However, thanks to a trick Peach and another character, Prince Peasley, created, Cackletta and Fawful had actually stolen Birdo's voice. Because of Birdo's squeaky voice, the Beanstar went crazy and broke into four pieces, which were scattered across the land. Mario and Luigi collect the pieces, and then travel to Bowser's Castle, where Cackletta, who had transformed into Bowletta, is. After a long battle, the Mario Bros. defeat Bowletta and save the day.
Unlike the last Mario and Luigi game, there are two new playable characters, Baby Mario and Baby Luigi. In this game, Mario, Luigi and their younger counterparts travel through time from the Mushroom Kingdom's past and present by jumping time holes.
One peaceful day in the Mushroom Kingdom's past, Baby Mario and Baby Luigi arrive at Baby Princess Peach's Castle for a playdate with Baby Peach. However, just as the Baby Mario Bros. arrive in her thrown room, Baby Bowser attempts to kidnap Baby Peach. Baby Mario, heroicly, steps up to fight Baby Bowser. Just after Baby Bowser's defeat, an alien race known as the Shroobs attack Baby Peach's Castle. A moment later, behind the clouds, hundreds of Shroob UFOS appear heading for the castle.
Back in the present, Professer Elven Gadd has finished his latest invention, a Time Machine. It's power source was the Cobalt Star. It was brodcast on live telivision at Princess Peach's Castle, Peach asked if she could try the machine. Peach, Toadiko, and Toadbert sent out to the past Mushroom Kingdom. However, Toadsworth, as always, is concerned if something happens. Even when E. Gadd said says he's 99% sure the princess will return, Toadsworth faints. Mario gets a Refreshroom from Toadsworth's room and gives it to Toadsworth.
The time machine returns after Toadsworth's recovery. However, it appears damaged. When the opens, Junior Shrooboid appears. Toadsworth and Luigi flee, but Mario, bravely, steps forward to defend the others and the castle. When a Toad goes into the time machine, Peach is nowhere to be seen. Luigi says a wierd hole appeared in the garden. Everyone heads for the garden. E. Gadd says the mysterious hole is a Time Hole which leads to the past of the Mushroom Kingdom, but there's one mystery. Where in the Mushroom Kingdom does it lead to? Luigi hops on the edge, but Toadsworth appears and accidently rams into into the Time Hole. Luigi is sent to the past, so Mario jumps in and is sent to the past as well.
Mario finds his brother next to the Time Hole. Mario and Luigi have been sent to Hollijolli Village. Shortly, a talking suitcase named Stuffwell appears. Stuffells says that the professor sent him to aid the bros. After teaching how to open and use items, the Time Hole disappears preventing Mario and Luigi from returning to their time thus trapping them in the past. The bros decide to deal with the problem later and explore the place where they are. After arriving in the village, they see all the villagers have been taken except the mayor. But the mayor is taken as well. Mario and Luigi engage the Shroobs in battle but are defeated after being blasted by a laser cannanball.
Above in the sky, the Koopa Cruiser is shot by Shroob UFOs. However, Baby Bowser has the Koopa Cannan fired. One of the pilots spots Mario and Luigi under attack by the Shroobs and asks if they should help him. But Baby Bowser says to ignore them. Baby Peach, upset that Baby Bowser is abandoning to help Mario and Luigi, throws a tantrum. Desperate to save his ears from the baby princess' crying, Baby Bowser fires the cannan at the Shroobs. Younger Toadsworth advises that more Shroobs might return at any moment and suggests that they take Mario and Luigi to the Koopa Cruiser. Toadsworth explains that the Shroobs came from a planet that was withering and decided to conquer the Mushroom Kingdom, turned the castle into Shroob Castle and told of their leader, Princess Shroob. Then, a transmission of Princess Shroob is seen. But the crew doesn't understand her language. One of the pilots says a Shroob Missile is heading shraight from Shroob Castle to the Koopa Cruiser. The Koopa Cannan was low on ammo. The Cruiser crashes into Bowser Castle. Mario, Luigi, Baby Mario, Baby Luigi, and the others head back to the present. Along the way, they find a shard. They decide to take it with them.
E. Gadd says that the shard they found was a piece of the Cobalt Star. The shard drives Junior Shrooboid crazy. E. Gadd suggest that the Cobalt Star might be the key to defeat the Shroobs and save the younger Mushroom Kingdom. Mario and Luigi decide to find the pieces of the Cobalt Star.
After finding five of the six shards, the four superstars head to Shroob Castle. In the statue of the shroob princess, they find Princess Peach. After taking care of the Shroob Mother Ship, Princess Shroob appears out of the rubble and appears to have gone insane. Princess Shroob battles the bros, but is utterly defeated. The plumbers and Peach find the almost complete Cobalt Star. Peach reveals to have the last shard, but says she can't allow it to be complete. Just before she could explain, Baby Bowser steals the last shard and puts it together. After it was whole, a dying Princess Shroob yells to it saying it's it's turn to fight the bros and calling it her sister before her death. Baby Bowser is turned into a shroob mushroom. Princess Peach explains that Princess Shroob has a twin sister and was trapped inside the Cobalt Star by Peach, but Peach was captured by the younger Princess Shroob. Since all the pieces of Cobalt Star were rebuilt, Elder Princess Shroob was able to be realesed from her prison. She mourns over her sister's death. Bent on avenging her sister, she fights the four heroes and Peach as revenge. Despite her best efforts and strength, Elder Princess Shroob was defeated and was turned in a mushroom which Baby Luigi claims. Princess Peach says even though the two shroob princesses are defeated, the Shroobs' foul work still plagues the whole kingdom and thier bane is still unknown. The Baby Mario Bros. start playing on the mushroom that was Baby Bowser, but Baby Luigi gets hurt and starts crying on the mushroom and Baby Bowser is returned to normal. Stuffwell contacts E. Gadd and tells the Shroobs' weakness is baby tears (water). E. Gadd sprays water all over the younger Mushroom Kingdom (also curing the victoms that were turned into Shroob Mushrooms).
As Profesor E. Gadd appears from the time hole and they return to the present. Mario, Luigi, Princess Peach, Toadsworth, and thier younger selves see Bowser lying on the floor in the throne room. Baby Mario jumps on Bowser. Elder Princess Shroob has Bowser eat her. Bowser is turned into Shrowser, everyone but Mario, Luigi, Baby Mario, and Baby Luigi flees. The bros easily beat Shrowser. Elder Princess Shroob's spirit explodes (thus leading to her demise) and Bowser is unconsioses on the floor. Mario, Luigi, Princess Peach, Toadsworth, and everyone bid farawell to Baby Mario, Baby Luigi, Baby Peach, and Younger Toadsworth as they return to the past.
Mario and Luigi once again went on another adventure when a mysterious disease called the Blorbs spreads across the Mushroom Kingdom, causing Toads to puff up to enormous sizes and roll around. Mario, Luigi, Princess Peach, and a new character, Starlow join to discuss the cause of the disease. During the meeting, Bowser barges in and attempts to kidnap Princess Peach, but he is beat by Mario and knocked out of the castle, while Luigi takes a nap.
Later, Bowser finds himself in Dimble Wood. After traveling around and learning all his moves, a stranger tempts Bowser to try a "Lucky" Mushroom. However, the "Lucky" Mushroom turned out to be a Vacuum Mushroom, and Bowser began to inhale everything around him. The stranger is later found to be Fawful. Bowser returns to Peach's castle and inhales everyone and becomes unconscious. Fawful takes over Princess Peach's Castle and Midbus takes over Bowser's Castle. Mario, Luigi, Princess Peach, and Starlow realize they are tiny and inside Bowser's Body! Mario and Luigi work together to help Bowser become conscious again. After Bowser awakens, he doesn't remember anything after being thrown out of Princess Peach's Castle or notice the Mario Brothers are inside of him. Starlow goes under the alias of "Chippy" to tell Bowser what happened. Bowser finds Fawful, who has already captured Bowser's Castle. Bowser must fight back for his castle, but with help from the Bros. inside of him.
Mario, Luigi, Princess Peach and Toadsworth take a trip to Pi'illo Island for a vacation. When they get to Pi'illo Island, Broque Monsieur and Starlow were already there. After exploring a bit, the Bros. find out Antasma have turned most of the Pi'illos into stone. Antasma then kidnaps Princess Peach and forces her into the Dream World. Mario must save the princess and the Pi'illos by traveling through Luigi's dreams and the rest of Pi'illo Island.
The Mario and Luigi series has, in general, unusually high review ratings for a video game series. Mario and Luigi: Partners in Time and Mario & Luigi: Paper Jam recieved slightly lower reviews Partners in Time due to its levels being rather linear, rather than like an RPG and Paper Jam due to the removal of several series staples such as the bonus level-up roulette, Toadsworth, several moves such as the Spin Jump, a detailed story, and it's lack of unique characters.
- Mario and Luigi have been in someone's body in every game in the series. They have been in Bowletta's body in Mario and Luigi: Superstar Saga, Yoob's body in Mario and Luigi: Partner's in Time, and Bowser's and a Sockop's body in Mario and Luigi: Bowser's Inside Story.
- In this series, Mario and Luigi lack the blue irises they have in the mainstream games and instead have black circles for eyes.
- There is always at least one Wiggler boss battle.
- Bowser is the Final Boss in every game. He has been Bowletta, Shrowser, Dark Bowser, and Dreamy Bowser.
- A castle is the last place to explore in the games.
- Every game starts at Princess Peach's Castle.
- When defeating the Final Boss, certain body parts must be beaten first to expose the weak point.
- All four games have a move where the player can drill into the ground.
- At least two new characters with at least a different speech patterns or language. Fawful, Cork, and Cask (Superstar Saga); Shroobs and Kylie Koopa (Partner's in Time); Midbus, Emoglobin, and Broque Monsieur (Bowser's Inside Story); and Anatasma, Big Massif, Lil' Massif, Bedsmith, and Nommons (Dream Team).
- When speaking, Mario and Luigi talk total nonsense about different types Italian pasta.