The main antagonist is Doomulus Wise, an intelligent, emotionally distant scholar who occupies a low position in their ranks. She's a member of a humanoid species with eight eyes, a tail, and antennae. Her plan is to build a laser that will fire at Earth from space, transforming its population into slaves for the Doomuli who will use the planet's resources and technology to advance the group.
She points out the weaknesses and failings of each member of the group, causing doubt. She also believes that controlling Earth's population isn't different from the injustices they've done to each other, and that it'll be beneficial in the long run, when the planet faces a threat that could destroy it.
In a final battle, the four defeat a powered-up Wise, who turns into a large insectoid creature with a Spirit Blump. After she reverts to her normal form, she activates the laser.
Spirit Blumps are rare Blumps that are gold and shimmer. Their effect matches the person's morality for an unexplainable reason. This allows it to mutate and deform the evil and heal or even resurrect the good.
As the laser is about to fire on Earth, Wise gloats that someone could disable it, but they'd die in the process (referencing Unten's choice not to save Zeon). Having grown, Unten decides to do it, and heads deep inside the laser. The others beg him not to, pleading that they can find another way. Speaking through the door, he tells them that it's his decision, and he's ready to die for the people and world he's come to love.
They flee the laser while Unten survives the treacherous inner layers of the machine. They make it off the laser, while he reaches the core and destroys it with his sword, telling Wise through a communicator that Earth is so much stronger than she knows. Her eyes widen and her mouth opens as the laser explodes, the blast knocking Unten out into space and vaporizing Wise with a wall of flame.
The others chase Unten's body as it falls to Earth, with Rachel sobbing and swearing that they can save him. They land in a wide open field, with the Beorn crashing beneath the shade of a tree. As the others approach him, Zerita quietly confirms that he's dead. She cries quietly while the other two are inconsolable.
From the skies, energy Elemental Blumps rain down. One lands near the group, and Bombyx grabs it, running over to Unten. Zerita asks what she's doing, with Bombyx saying that they know it has healing properties, so perhaps it can do someting. Sure enough, squeezing its juices into Unten's mouth resurrects him.
The game is a cel-shaded 2.5d platformerthat features movement similar to the 3D games in the series and a health bar that's exactly the same as the one in Super Mario Sunshine.
The game's plot has Mario being called back to Isle Delfino by E. Gadd, who informs him that goop has returned to Noki Bay. He suspects Bowser and his son are up to no good, and sends him to investigate. To assist in his mission, Gadd gives Mario his newest invention: the Goop Suit. It allows him to absorb goop and use it to his advantage.
Mario eventually learns that Gooper Blooper is the culprit, and his plan is to drive out the Nokis and turn the bay into a Blooper habitat. He's accomplished this with the Goop Staff, a magical Noki artifact. Mario defeats Gooper Blooper, in his normal state and a powered up form, and uses the staff to restore Noki Bay to normal. Gadd builds a new home for Gooper Blooper where he and his friends can live.
Mario then heads home after returning the suit to Gadd. While on the flight, Gadd informs him that suspicious activity is going on in Bianco Hills.
The game's main new mechanic is the Goop Suit. By touching goop, Mario will fill up a meter. With it, he can double jump, throw bouncy goop balls, slide faster, send out a stunning wave of goop, create temporary platforms, and clear the screen with a goop powered ground pound.
Although he starts with the double jump alone, he can learn more of these abilities by finding the Noki Elder, who is hidden in some stages.
The game has nine areas, one of them unlockable: Sunshine Port, Sapphire Sea, Waterfall Mountain, Dark Depths, Ancient Ruins, Royal Tomb, Seashell Towers, Cloudy Skies, and the Secret of Noki Bay.
The game's nine bosses are: Hopper the Giant Cheep Cheep, Maw-Ray, Cannon Mole, Eely Mouth, Inky Piranha, Sludge Boo, Gusty the Wind Spirit, Gooper Blooper, and Powered-Up Blooper.
Each miniboss is a different version of the Polluted Piranha Plant.
In the Secret of Noki Bay, Mario cannot use goop abilities.
To unlock this secret world, Mario must collect every Shine Sprite scattered across the areas.
A Tanooki runs a shop where coins can be used to buy items.
Blue coins are worth 5 coins and red coins must be collected to gain an item.
Lives have been eliminated entirely, after every death, Mario will be returned to the last Pianta Flag he passed. To compensate, this game is more difficult than the past few 2D entries.