The Dark Domination is the story mode for Megald Warriors.
Megapolis Part 1
Mario and Megaman are sitting on a bench chatting when suddenly they get swarmed by Dark Matter spawns. After defeating them, they see a Dark Matter Ship up above and notice that more Dark Matter spawns are coming down from the airship. A Dark Matter clone of Mario appears, and he defeats the two and takes their trophies back to the airship.
Realm of the Gods
Meanwhile, at the Realm of the Gods where the higher deities reside, Pit and Thor are guarding the council room. They come across an army of Elves, and the two manage to defeat them. They then realize that more Elves are invading the council room, however a mysterious ninja named Sheik manages to fight off some of the Elves. They then meet with Palutena, one of the higher deities, who instructs them to inflitrate the Dark Matter Airship. Pit nods and he flies the team onto the Airship.
Doofenshmirtz Evil Inc.
Dark Matter is meeting with Zim and Dr. Doofenshmirtz to discuss their plans of world domination. Agent P overhears, and attacks Zim and Dr. Doofenshmirtz, defeating them both. However, Dark Matter enters Agent P's body, possessing him. Dark Matter!Agent P launches more airships all across Megald.
Dark Matter Airship
Pit, Sheik, and Thor enter the Airship, and fight off Elves and other minions along the way. They try to enter the Trophy Room, but Koopas are guarding the entrance. After defeating the Koopas, the three enter the trophy room and revive Mario and Megaman. However, the five are surrounded by Elf Troops, and they jump out of the Airship as a last resort, landing somewhere unknown.....
Ruby Rose and Weiss Schnee find themselves deserted at the forbidden forest. Weiss is quick to blame it all on Ruby, and the two get into a fight, but are swarmed by Beowulves. After defeating the Beowulves, the two see more Dark Matter Airships heading towards Beacon Academy. The two decide to follow the airships to see if they can get any help.
The Critic's House
Meanwhile, The Nostalgia Critic is still trying to recover from his Food Fight review, when suddenly he is attacked by Dark Matter. The Critic goes crazy and defeats them all. Captain America walks into the house, startling the Critic. Captain America tells him that they need him to stop Dark Matter, and the two get on the Helicarrier.
Megapolis Part 2
Dark Matter now controls Megapolis, and it's powers begin to spread out into other parts of Megald. Emily and Leon Redbeard arrive and attempt to fight off Dark Matter's forces, but they are outnumbered and outmatched. However, the Helicarrier swoops in and it is revealed that they have reinforcements. Iron Man, Black Widow, Green Lantern, and Samus jump down from the Hellicarrier and assist the two in battle. After defeating a significant portion of Dark Matter's forces, the Hellicarrier swoops down and picks up Emily, Leon, Iron Man, Black Widow, Green Lantern, and Samus.
Barry Bee is relaxing at his house in the Bee Hive when Silver teleports in, claiming that he came from the future to save Megald from destruction. The house gets invaded by Elves, but the two defeat them. Silver then teleports himself and Barry to Green Hill Zone.
Green Hill Zone
Silver and Barry teleport to Green Hill Zone, which is where Mario and the group landed. Silver and Barry team up with Mario's team, and they fight off an army of Elves, Badniks, Beowulves, and more enemies. After defeating the army, The Hellicarrier comes and picks up the team.
The Mystery Shack
Ruby and Weiss follow the Airship and find themselves at the Mystery Shack, where Dipper and Mabel are fighting off an army of gnomes led by Gideon. The four defeat Gideon and Mabel grapples onto the airship with Dipper, Ruby, and Weiss.
Aboard the Helicarrier
Sheik transforms into Zelda, not feeling the need to hide her identity anymore. The Helicarrier gets into a dog fight with a group of smaller airships when they find out that they're out of ammo. Suddenly, the airships get knocked away by a sandstorm. It then shows Gaara on top of the Helicarrier, who was the cause of the sandstorm. The team lets Gaara inside the Helicarrier and he joins the team.
The team decides to split up into two groups of eight: The Nostalgia Critic, Gaara, Captain America, Barry, Leon, Emily, Megaman, and Thor stay on the Helicarrier and reload ammo to take down enemy ships. Mario, Silver, Iron Man, Green Lantern, Zelda, Samus, Pit, and Black Widow go out and try to stop Dark Matter's forces.
In a conference room, a small group of villains from comics are having a meeting. Two-Face, Magneto, Deadpool, and Moe are all present, when suddenly, Alpha bursts in and attacks the group. After defeating the villains, Alpha realizes that the Conference Room is about to self-destruct. Donkey Kong bursts in and helps Alpha escape, and the two meet up with Mario, Silver, Iron Man, GL, Zelda, Samus, Pit, and Black Widow.
Meanwhile in Elsa's Tower, Elsa is fending off an army of soldiers led by Prince Hans, who appears to be affilliated with Dark Matter. Rosalina comes down to assist her, and the two defeat Hans and his soldiers. After the battle, Rosalina informs Elsa that her sister Anna has been captured. The two escape the tower and set out.
Dipper, Mabel, Weiss, and Ruby get picked up by the Halberd, where Meta Knight informs them about Dark Matter's invasion. Soon the team is attacked by Magolor, who is possessed by Dark Matter. After defeating Magolor, they return him to his normal state. The team goes to pick up Elsa and Rosalina before heading into the heart of Dark Matter.
Mind Control Chamber
Mario and his team enter a Mind Control Chamber, where they fight Greninja, Yoshi, Anna, and Unten, who have all been mind controlled. After defeating them, they reverse the mind control and revive them. However, the team is then surrounded by minions, whom they quickly defeat. Soon, 0² appears, and turns them all into trophies.
He destroyes the Halberd and Hellicarrier, and traps Dipper, Mabel, Ruby, Weiss, Meta Knight, Magolor, Elsa, Rosalina, The Nostalgia Critic, Gaara, Captain America, Leon Redbeard, Barry Bee, Emily, Thor and Megaman in an endless limbo. He then sends an army of Dark Matter soldiers, led by Gavin Sparrow and Elec Man, to dethrone the two main deities of Megald (Palutena and Raiden) and strip them of their power. Now Dark Matter forces are sent out to either enslave or destroy any remaining heroes.
0²'s plan succeeds, giving him complete control over Megald. It's all over now.
.....or is it?
Dumpster Part 1
0² has successfully conquered Megald, and now Calvin & Hobbes and Villager, among many others, are left as slaves, clearing out the dumpster. The two notice Pink Gold Peach attacking her human counterpart, Princess Peach, and decide to go help her. Calvin & Hobbes, Villager, and Princess Peach defeat Pink Gold Peach but then are ambushed by an army of Dark Matter beings. After defeating them, the team escapes the dumpster and tries to find more heroes.
Zim and Dr. Doofenshmirtz are in the Lab with the trophies of Mario, Samus and Alpha, when Zim reveals that he is a double agent and turns Dr. Doofenshmirtz into a trophy. Zim revives the trophies of Mario, Samus, and Alpha and the team confronts Dark Matter!Agent P, who sends Toon Donkey Kong, Stockart Squav, Gavin Sparrow, and Takeo Yumi out to defeat them. The heroes win, and the team turns Stockart Squav back into Squav, who joins the team. The team fights Dark Matter!Agent P, and after the heroes win the battle Dark Matter flees out of Agent P's body. Samus' armor breaks down, turning her into Zro Suit Samus, and the heroes revive Agent P.
Dumpster Part 2
Calvin, Hobbes, the Villager and Peach keep exploring the Dumpster, where they come across the trophy of Silver, and they revive him. Silver begins to explain his plan, but the team is ambushed by Dark Matter's forces. After the battle, Silver creates a portal, and he and the rest of the team go through.
Silver's team ends up in what used to be the Throne Room of the higher deities. Swordsman Darkmatter stands in the throne that once was Palutena's, and the team fight him and defeat him. After the battle, Silver sets free the deities Palutena and Raiden, who have now regained their powers. The team then goes through a portal.
Meanwhile, Meta Knight and the others are trapped in Limbo when suddenly Eren Jeager, Ike, Scarlet Witch, and Quicksilver warp in and explain that Silver gave them power to detect warp through limbos. However, Dark Matter's forces quickly arrive, and the four defeat them, and the whole team warps out of the limbo.
Dr. Wily's Factory
Mario's team enter's Dr. Wily's factory, where Dr. Wily reveals that he has the trophies for the rest of Mario's team (Greninja, Yoshi, Anna, Unten, Green Lantern, Iron Man, Pit, Donkey Kong, Black Widow, and Zelda) after facing the Yellow Devil and later Dr. Wily, the team revives the trophies and ,after a little bit of platforming, goes through a portal.
In Bugs Bunny's house, Bugs Bunny is reading a newspaper article when suddenly he gets a distress call from Silver, giving him certain coordinates. He gets ambushed by Dark Matter forces and meets up with Wily E. Coyote, who go to find Silver's coordinates.
Mario's team, Silver's team, and Meta Knight's team all meet up at the Battlefield, where a gigantic army of Dark Matter spawns, Koopas, and other enemies attack them. The heroes are losing at first when suddenly a huge army of heroes comes, led by Bugs Bunny and Wily E. Coyote. Silver reveals that the coordinates he gave Bugs led to a secret trophy stash made by the villains, storing the rest of the heroes' trophies. After the battle, a hologram of 0² appears and taunts the heroes, and teleports them to Final Destination, where the final battle begins...
The heroes are teleported to Final Destination, where 0² is waiting. The heroes fight 0² and win. After the battle, Raiden and Palutena cast away any trace of Dark Matter, including 0² himself, and Megald is safe, for now.
The heroes go back to Megapolis to celebrate, unaware that a new evil is rising.....
END OF STORY MODE