Rosalina says to journey to a distant land called Nargard, where a man named Carlo has knowledge of Marmian and may be able to help. Rosalina introduces Io, an experienced archer, to help Mario and his friends on their journey. Rosalina tells Toadsworth to stay at her kingdom so he can help her out with building a well made defense system.

Mario, Io, Luigi, Toad, and Yoshi begin to sail to Nargard along with some of Rosalina's star minions. Along the way, they encounter many lethal creatures that attempt to bring the boat down. After battling Asermety, the first big boss of the game, the boat is badly damaged and nearly sinking. They drift to an unknown island and jump and swim to it as the boat sinks. When they arrive at the island, they find that it's infested with creatures called Necroromblis', which are paranormal beings that can take shape of anyone they touch. Many stars are killed.

Luigi and Toad are captured and leave Mario, the last surviving star who came along who's name is Apron, Yoshi, and Io to battle the Necroromblis'. Mario then battles another boss named Mystery, soon defeating him.

Then, a tribe of people called the Coroms approach Mario, Yoshi, Io, and Apron. They're curious. They've feared the Necroromblis' for years and welcome the four of them into their lair. They meet the leader of the Coroms named Riff and his right hand man named James, who let's Mario, Yoshi, Apron, and Io stay warmly. Io then tells Riff about their journey and what's at stake. Riff tells of a distant ship, that they could leave on, but was always impossible to get to since the Necroromblis' nest is in the area that the boat is. Riff then tells them that there is a coat of armor that will make them invisible to the creatures and that they must collect five different star pieces from around the island to create it.

Mario and Io go to find it and split up so they can cover more ground. Mario, after a long and tiring journey, manages to find four of the star pieces while Io finds the other.

They create the coat of arms back at the Coroms' lair and Mario, Io, Riff, Yoshi, James, and Apron journey into the nest while Mario wears the coat of arms. If anyone is standing near someone that wears the coat of arms, then they too, will be invisible.

When they get to the boat, Mario, Yoshi, and Riff stay behind to find Luigi and Toad while the others sail the boat around the island to retrieve all the Coroms waiting on the other side that's safe. They barely escape since they didn't have the coat of arms anymore.

The three of them eventually find Luigi and Toad, but then, the coat of arms wears off and the Necroromblis' attack them. Riff is killed as they escape and the rest barely make it out.

After mourning Riff, they walk to the safe side of the island and see that the ship made it out and that they're all waiting for them on the ship. They set off to the city of Nargard.

Meanwhile, Peach and Daisy are captives at Bowser's high tech castle that is floating in the air over a distant ocean. Daisy and Peach are brought to Bowser's throne. Bowser tells how he needs them to make a deal with the terrifying creatures of Nightmare Valley for the biggest Marmian they have that could destroy the world. Nightmare Valley wants them because of their power. Their power could help Nightmare Valley strive.

Bowser reveals that Marmian will wipe everything out except for specific coordinates that he marks, so that he and his minions will live. Karem, a nasty, horrible, snakelike man who's Bowser's new top minion, leads them back to their cells to wait for the trade.

It then shows Mario's ship arriving at Nargard. It's a nice, peaceful city with nice people. After the Coroms are welcomed as citizens, Mario, Luigi, Yoshi, Io, Toad, James, and Apron travel to city hall and meet the mayor, Mayor Strizan. They ask where Carlo is and he explains that Carlo is a well respected italian man of the town who strives in his company which makes boats.

They travel to his condo and meet and greet him. They meet his servant, Hugh, who is the best swordsman of all time.

As they talk, Carlo then tells Mario and Luigi that he is their long lost brother. After a lot of questioning, James takes a blood sample and finds out that he is their brother. Carlo explains that their parents banished him from the Mushroom Kingdom after he protested against a war that their parents were leading. Carlo has a yellow suit like how Mario and Luigi have red and green suits.

Soon, Carlo tells them of the energy source of Marmian, and how he encountered it once. Marmian was being smuggled through his old city, and he went undercover to investigate it. He tells what Rosalina told about how powerful it's fission reaction is. Carlo then says that the man who created it is located in a cave on a distant subcontinent called Vagerical, and he can possibly shut down the source that's powering Marmian.

Carlo and Hugh join Mario's group and ride giant birds called Remers to Vagerical. Along the way, another boss called the Weather Maker creates storms and shoots lightning at them.

Carlo proves himself to be quite a good fighter and defeats the
Weather Maker with a trident that's also a lightning rod. Mario and Luigi begin to trust him a bit more and respect him a lot.

They occasionally stop at different towns and cities. As they stop at a city called Winer, dozens of flying ships invade. Donkey Kong is leading the fleet of ships. It's then that Toad's skin melts off and reveals himself to be a Necroromblis who took Toad's shape before brutally murdering him at the nest. He did this when they captured him.

The Necroromblis secretly led the fleet right to them. Hugh, completely angered, fights him with his sword. His skills with the sword are remarkable. As Luigi, James and Yoshi help Hugh out, Carlo leads Mario, Apron, and Io to the ships to take them down.

Carlo has a great knowledge of stealth and silently leads them through the city, snapping some enemies' necks as they attempt to kill civilians.

The four of them take control of one ship and has an aerial fight with the others. Soon, Donkey Kong's ship is the last one standing.

Mario boards and has a boss fight with Donkey Kong. He manages to exhaust Donkey Kong, who cowardly makes a run for it.

They return to see that Hugh has been killed and see that the rest of them were captured by the Necroromblis.

Mario, Apron, Io, and Carlo attempt to chase and catch him, but can't catch up. They had no choice but to move on.