The story for Hellfire Fighters 2. It involves the team facing Bill Cipher, who was the one behind the battle with XANA in the first game.
Part 1: The Forming
The story begins in a dark place. Bill Cipher slowly fades in, and summons his three main generals: Herobrine, Bowser, and Eggman. He asks if XANA succeeds, to which Herobrine replies "no." Bill Cipher than says he'll have to get rid of the heroes himself, and he will rule the universe, "as it was meant to be."
The scene changes to Mario's house. After the long battle with XANA, Mario invited Sonic over to the Mushroom Castle. They were about to start watching a movie when suddenly, they heard a deafening explosion. Mario and Sonic went out, to see an Arwing having a dogfight with a few strange airships. Each airship had an eye painted just above the cockpit. After all the airships are shot down, the Arwing came down, and Fox and Inori Aizawa come out and explain an evil is rising and they have to stop it. The four get into the Arwing and start their mission.
Meanwile, Twilight Sparkle is walking around Ponyville with Fluttershy and Rainbow Dash. Out of nowhere, a car constructed entirely out of candy drives past the trio. Vanellope gets out of the car and teleports around the ponies. Rainbow Dash gets annoyed and tackles into Vanellope. A battle begins between the three ponies and Vanellope. Once defeated, Vanellope will tell the trio of a strange power rising in Diet Cola Mountain. The ponies hop in Vanellope's car and they head in the direction of Diet Cola Mountain.
Meanwhile, Bass and Metal Sonic are kidnapping people around. They knock on Mario's house, only to find Luigi standing in the doorway. They knock him out, and take him to their base.
Alpha comes into ;Mech City to find all of the buildings griefed. He thinks Rockoon is the main suspect, and he decides to go after him. After a long search through ;Mech City, Alpha finds Rockoon and proceeds to battle him. But, after defeating him, he realizes Rockoon isn't behind the griefing. Alpha decides to meet up with his friends when suddenly, he gets sucked through a portal.
Diet Cola Mountain (Boss Area)
Fluttershy, Rainbow Dash, Twilight Sparkle, and Vanellope arrive at Diet Cola Mountain, which is hooked to a power draining machine of sorts. They find out a triangle-shaped villain is behind this, along with a robot version of Vanellope. They both fly away from the scene, and leave the four there to fall in the volcano. They actually do, and land on the testing track that Ralph once made. Suddenly, the machine bursts apart, revealing a revived Ridley. The Space Pirate grabs Vanellope, and takes her to the top of the volcano. Because of this, the ponies must follow Ridley, and save Vanellope!
Once Ridley is beaten, he'll fall into the volcano and die. The heroes are rewarded with a Chaos Emerald, which was used to power the machine.
Calvin and Hobbes are watching a TV show when their dad comes in and shoos them out. Calvin sees the Killer Bike, who starts glowing. Suddenly, out of nowhere, he runs over Hobbes, turning him into a trophy. Calvin chases after the Killer Bike, but it teleports away, taking Hobbes with him. Calvin turns around and sees Alpha come out of a portal. Calvin thinks it was him who hired the Killer Bike to take Hobbes, and after the battle, the winner sees Bill Cipher's fleet arriving and revives the loser, and the two head out.
Link is sitting in the field, playing his Ocarina. It's been awhile since he last saw his "friends" and he was sort of lonely. But he still had Zelda...somewhere. Suddenly, it seems like the Sun is getting closer, when something falls out of the sky. It turns out to be a cross between a unicorn and a cat. The Uni-Kitty mistakes Link for a villain, and the two engage in battle.
When Link beats Uni-Kitty, a scream is heard from Hyrule Castle. The two team up, and run to the source.
Hyrule Castle (Boss Area)
When the new duo arrive at the castle, we can see Dwight Tharp getting shoved into a wall by King Dodongo, while Princess Zelda is trying to stop him. King Dodongo notices Uni-Kitty out of the corner of his eye, and he charges at her, when Link fends off the giant beast. The battle then begins.
When King Dodongo is beaten, he'll gag a bit, eventually coughing up Origami Yoda, and exploding. Zelda thanks Link and Uni-Kitty, joining them. Suddenly, another portal appears, and the crew walks in.
The Great Tower Of Bowser Land (Cutscene)
When we see the tower, we can see Bill and Dimentio at the bottom of the tower, rambling on how Bill will team up with another villain. Dimentio tells Bill it's time, and Bill shoots a ray of light at Bowser Land, turning it into a Cipher-filled paradise.