Template:The Quest Begins

The remaining characters find themselves alone in the desert after the Chaos Ones flee. They quickly leave the desert and head to the Providence Board Room. They have a meeting and decide that their first order of business is to figure out what in the world is going on. They decide to send Sonic, Shadow and Jet to follow the Halberd as it approaches its destination, Metropolis. The three friends leave and head down into the city. The cross the city but run into Link battling Ganondorf. They help link stop Ganondorf, but cannot stop him from using a Chaos Cannon to turn Jet into Chaos Jet and Shadow into Chaos Shadow. He leaves, satisfied with having created two more Chaos Ones. Sonic and Link then continue their quest. (Name of Stage: The City)

Back at the Providence Board Room, the heroes decide to send Peach and Zelda to Peach's Castle, so they can round up supplies. They leave and take a ship to cross the desert. When they land in Toad Town, they find Wario and Waluigi reaking havoc. They stop the two fiends and contineu on into the castle They head throughout the whole castle slowly making their way to the throne room on the fifth floor. When they reach the throne room, they find metal Sonic with a Chaos Control bomb sitting on the throne. He activates the bomb but soon Silver and Blaze arrive on the scene to stop him. They are unable to stop neither Metal Sonic nor the Chaos Control bomb. The five characters, good and bad, are teleported to Angel Island, and Peach's Castle is destroyed. (Name of Stage: Peach's Castle)

The next group of people to leave is the group of Ben Tennyson, Kevin Levin, and Luigi, who go back to Bellwood to investiagte a mysterious creature that has been spotted. When the three arrive, they find Gwen Tennyson battling Pikachu, Lucario and Jigglypuff. After all three pokemon are defeated, a Pokemon Trainer appears a recaptures them before running off. Wondering why he did so, the four heroes chase him through the city. When they catch up to him, they find that he actually Chaos Pokemon Trainer, as turned into by Bowser Jr. He activates a Chaos Control bomb, teleporting them all to Los Soledad. (Name of Stage: Bellwood 2).

Ness and Lucas, the only characters left at providence find a left over Chaos Control bomb that was placed their by Bowser. The bomb detonates, destroying Providence and teleporting Ness and Lucas high in the sky. They wake up right infront of Pit. They follow him through Skyworld and eventually find themselves helping out. They reach a castle, but the castle is locked. While Pit searches for a key, Ness notices the Halberd flying through Skyworld. The three heroes then have 3 minutes to complete the next part of the stage and board the Halberd. Once on the Halberd they hide on the lowest deck. (Name of Stage: Skyworld)

Back in Dry, Dry Desert, the villains find themselves beaten. Vilgax, Van Kleiss, Biowulf, and Bowser then decide to take their revenge on the Chaos Ones for not helping them in battle. The notice that Providence has been destroyed and the head to the ruins. Once at the edge of the ruins, they find Midbus. Realizing that he knows they are betryaing Fawful, they attack, but are no match for him. He defeates them all, and turns them into Chaos Vilgax, Chaos Van Kleiss, Chaos Biowulf, and Chaos Bowser. He then takes them all back to Metropolis. (Name of Stage: Providence Ruins).

In Los Soledad, Beb, Gwen, Kevin and Luigi split up. Gwen and Kevin take the southern section and find nothing. Ben and luigi take the northern section and find nothing at first, but after a little more in depth searching, find Professor Paradox. The three head back and find Gwen and Kevin. The five then go into the southern section again, this time finding Donkey Kong and Diddy Kong. All seven heores decide to rest for the moment, but realize that they will have to set out very quickly. (Name of Stage: Los Soledad).

On the lowest deck of the Halberd, Lucas, Ness, and Pit are discovered by Chaos Mario. They outrun Chaos Mario, but find themselves right in front of Main Cannon #1, which has been converted into a Chaos Cannon. They are about to get blasted by the cannon when Kirby and Meta Knight appear. The player can choose either character to battle the other. The winner will save Lucas, Ness, and Pit. The loser will fall right in front of Main Cannon #2. After the battle, Lucas, Ness, Pit, and Kirby/Meta Knight will go across the Halberd. If the playuer has Kirby, they will take over the control room and force the ship to crash. If the player has Meta Knight, they will take of the control room and defend off a siege from the Chaos Ones, only having to battle three of them, chosen at random. If the ship crashes, the heroes will flee and head into Los Soledad. If they take over the ship, the Chaos Ones will flee and the ship will land in Los Soledad. (Name of Stage: Halberd 2).

Peach, Zelda, Silver and Blaze wake up on Angel Isand and chase Metal Sonic all the way to the citadel. They battle him once they chase him down and defeat. However, he still takes the Master Emerald and flees. The island starts to fall out of the sky resulting in the loss of the Master Emerald. Before it crashes, the heroes recieve help from Samus and slowly bring the island to the ground just inside the boundaries of Los Soledad. (Name of Stage: Angel Island).

Meanwhile, Sonic and Link find themselves running through a jungle folllowing an energy signature of the Chaos Emeralds. While in the jungle, they find Ike and Marth follwing the same source of energy, although they don't know what if is. The four heroes team up and make their way out of the jungle, only to find Ganondorf again with a Chais Control bomb. He activates the bomb the flees. The bomb sends them all to Los Soledad. (Name of Stage: The Jungle).

Finding all the heroes at Los Soledad, they realize that they are basically back to square one.