After finishing up a meeting, Peach is contacted by Zelda via telepathy, having heard rumors about Billy from who-knows-where, and after being requested to, Peach begins telling Zelda the story...
Meanwhile, at Bowser Castle, the Koopa King waits impatiently for the other villains to arrive. One of the villains does arrive: Mewtwo, who quietly teleports there. The next arrival is a bit louder, as Ridley arrives from the sky with a roar. As both villains enter the castle to wait for the others, 3 more villains arrive: Star Wolf (To Bowser Jr's delight). Then comes the loudest entry: King Dedede, who even has two Waddle Dees herald his arrival... though both of them are promptly knocked away by King K Rool making his entrance... only to be flattened under Dedede's weight. After keeping the two overweight Kings from clashing by threatening them with his fire breath, Bowser is met with the final villain to arrive, one who he's not happy to see at all... Ganondorf. The King of Evil's taunts provoke Bowser into trying to attack him, but Kamek prevents a fight from breaking out, and calms Bowser down, but even then, Bowser can't stand to even look in Ganondorf's direction as Kamek escorts him inside.
Meanwhile, back at Peach's Castle, Peach finishes telling Zelda the story. Since Billy's not present at the time, Peach and Zelda arrange for Peach and Billy to go to Hyrule Castle for dinner, so Zelda can meet Billy in person. With that, Peach and Zelda's conversation ends. Peach has two Toads prepare for the trip, while Toadsworth isn't 100% on the plan. Peach states that it's fine, as nothing can go wrong.
The next day, Peach is shocked to find out that something went wrong: The only plane currently available is broken. As there are no Warp Pipes leading to Hyrule, and Hyrule doesn't have the technology for Peach to call and reschedule, they take the last option available... A dangerous trek through Hyrule Forest. Having no other choice, Peach decides to invite Mario along for protection, while Toadsworth stays behind due to having... Paperwork to attend to.
Back at Bowser's Castle, the villains are at first shocked by Bowser's (reluctant) offer of a Team-Up, with Ganondorf starting to taunt him for needing them to get anything done. Kamek calms the villains down, and Bowser begins to explain the Gospil Seed to the other villains, but not before having Junior leave the room, due to this being an "adult conversation"... which Junior couldn't resist peeking in on once he's out of sight.
Meanwhile, as Peach, Mario and 2 Toads trek through Hyrule Forest, the Toads begin having second thoughts about the whole ordeal, as two shadowy figures watch from the trees... Later, as the trek continues, the group is ambushed by a bunch of Deku Scrubs who overwhelm Mario. Just as a large, club-wielding enemy prepares to strike Mario down, the shadowy figures, revealed to be Donkey Kong and Diddy Kong, come to the rescue. During the skirmish, a stray Deku Seed flies into Billy's mouth, who realizes how tasty it is, and promptly begins chowing down of the Deku Scrubs, to the shock of everyone present.
Meanwhile, Bowser has just finished informing the other villains about the Gospil Seed... only for each and every one of them to start to rush out of the room to claim the Seed for themselves—- Only to be stopped in their tracks by Mewtwo. The cloned Pokemon points out that all Bowser told them was that the seed is in a Piranha Plant, but not which one it is in specifically, and Bowser would've beaten the lot of them to the seed, since he's the only one who knows its location. After Bowser confirms he was going to divide the power equally, the villains finally agree to the Team-Up, and Mewtwo unfreezes all of them... except for Ganondorf, who jokes that it's wise not to trust him. Bowser seems ready to bury the hatchet in favor of taking over the world, and after reluctantly agreeing, Ganondorf is unfrozen. Bowser then begins going over the plan...
Back in Hyrule, Peach, the Toads, Billy, DK, Diddy & Mario, still exhausted from the previous ordeal, have all reached Hyrule Castle Town, though DK and Diddy can't stay due to Cranky Kong needing help testing his potions. Zelda is shocked that the group went through Deku Forest and put themselves in harm's way, and makes Peach promise not to do that again.
Unaware to all of them, coming home might be a bigger danger than the Hyrule Forest...
Meanwhile, on the outskirts of Peach's Castle, Bowser and Star Wolf begin the final preparations for the siege: Leon watches in amazement as Bowser's Boos make a large group of minions disappear. Bowser is introduced to Ridley's lieutenant, Armados, who is in charge of sneaking another group into the castle. Back at Bowser's Castle, Kamek's magic and Mewtwo's psychic powers create a full scale map of Peach's Castle, effectively making it so that there's nothing in the castle the villains won't know about. And with that, the siege begins.
Armados leads one group inside, while a Bronto Burt signals another group in through a window. After both groups are in each other's vision, the villains make themselves known and start rounding up the helpless and unprepared Toads, who are stopped from fleeing at every turn and crowded into a tiny room (which Toadsworth happens to be in). After reporting to Bowser that the castle is secure, a Goomba and a Waddle Dee break him some bad news; neither Peach nor Billy are in the Castle. After planning to ambush them when they return, there's a knock on the door, and the villains send out a Toad to answer it. It turns out to be Morty Boomer, the Boomerang Bro, Jetpack-equipped assistant to Prof. E Gadd, who's delivering a package Toadsworth ordered. However, when Boomer asks for a signature, he is surprised to find an SOS message. He hastily flies off to deliver it, but is promptly shot down by Armados, who takes a small squad of minions out to grab the Bro. Meanwhile, the injured Boomer sends out a distress signal, both for himself and for the residents of Peach's Castle.
Meanwhile, Boomer's distress signal is retrieved by none other than Star Fox, who pinpoint the location to the Mushroom Kingdom. After debating what it could be about, due to the Mario Bros normally handling things there, Fox and Falco depart to investigate.
Meanwhile, Armados and the two minions he took with him close in on Boomer, but are forced to remain in the shadows when Fox and Falco arrive. After Falco finds and questions Boomer, Armados and the minions make themselves known and attack. After a quick battle, Armados is driven off when Fox places a bomb (given to him by Boomer) on his back. After Boomer informs them of all he knows about the situation, Falco heads to Peach's Castle, while Fox heads to Mario and Luigi's house to get help from them.
Fox finds Luigi, and is told about Mario and Peach's trip to Hyrule. Fox tells Luigi that something's wrong with Peach's Castle, and departs for Hyrule to warn Peach. A curious Luigi then starts a trek to the castle...
Later, Falco lands in front of the castle, and after barging past the Toad at the door, demands to know what's going on... and is promptly surrounded by all the villains and their minions, who were warned by Armados beforehand, and Falco is beaten up. Luigi arrives shortly afterwards, and immediately meets the same fate. They are soon tied up, but a gloating Bowser unknowingly lets slip the existence of the Gospil Seed.
Meanwhile, over in Hyrule, Fox finds from a guard that Peach, Zelda and the others are out for a walk. Later, while Fox is flying above Hyrule, trying to find them, he spots Link's house. After discovering that Peach and Zelda aren't at Link's House, Fox receives a call from Falco, who informs Fox of the situation at Peach's Castle, before getting discovered by a Koopa and being relieved of his codec. Fox prepares to return to the Mushroom Kingdom, with Link tagging along.
Later, at Peach's Castle, the duo sneak in via a Warp Pipe into the kitchen, where they discover a Waddle Dee making chili in a pot. After the Waddle Dee leaves, Fox pours a whole bag of Morty's bombs into the pot. Proceeding into the hallway, the duo overhear a Koopa telling a guard not to let Falco and Luigi out of the room. Now knowing where to go, Fox thinks about how to sneak past the guard. The duo are soon discovered by a Goomba, who Link silences by stuffing a bomb in his mouth, then throwing him past the guard. When the guard goes to investigate, the duo sneak by him and free Falco and Luigi. After a bit, they discover the room where the Toads are locked up. After Toadsworth stops Falco from breaking down the door because it's expensive, he suggests they find a key.
After sneaking around the castle a bit more, they eventually find a key... unfortunately, it's in the hands of Bowser. Even more unfortunately, Bowser and Star Wolf know that Luigi and Falco are free. Even more unfortunately, the quartet are immediately discovered and surrounded by ever minion in the castle. However, it's here that Fox reveals his ace in the hole... He detonates the bombs he pored into the chili earlier, causing every minion present to flee. Enraged by this turn of events (And the fact that it's implied that Bowser ate more chili than anyone else,) Bowser and Star Wolf attack. During the skirmish, Falco manages to obtain the key to the hostage room... which proves irrelevant, as Bowser accidentally destroys the door moments later.
After a long skirmish, the heroes finally come out on top and fling the villains out of the castle. As Wolf sarcastically congratulates Bowser for his "fool proof plan", they are caught by Slippy and Krystal... but Mewtwo teleports both villains away before they can be brought in.
After the fight, the away party appears in the main hall, having been teleported home by Zelda, who is surprised to see Link there.
