Kirby- The main protagonist of the mini series along with the Sonic X version of Sonic.
Sonic- Hero of a planet that is presumed to be called Mobius (since Sonic X never mentioned the name of Sonics world).
Tokkori- Kirby's somewhat pet bird and roomate. He mostly fits into places Kirby won't fit in.
Miles "Tails" Prower- Sonic's best friend and sidekick. Tails mostly uses the tornado for battle except in this mini series.
Tiff- A girl with some great intelligence and some anger issues. Tiff helps with solving puzzles or riddles.
Knuckles- Guardian of the Master Emerald on Angel Island. He is sometimes bent on protecting the Mater Emerald no matter what.
Tuff- Tiff's younger brother and sometimes mischief maker. He uses his slingshot to press buttons that are hard to reach.
Amy Rose- A pink Hedgehog with anger issues, and Sonic's "self proclaimed" girlfriend. Amy can use her hammer on enemies that attack her or make her angry.
Marx- After his defeat in Issue 25, he has stumbled upon another sorcerrer in the far reaches of space. He is one of the two main antagonists of the mini series along with the Sonic X version of Ixis Naugus (if he appears in that show).
Ixis Naugus- An evil sorcerrer that has ended up in space longer after his defeat from Sonic. However, that space is in the Kirby universe and in there longer than Marx. Naugus then encounterd Marx and joined forces to merge the two Universes Together.
1- Each of the Universes have doors with stars on top of them and they lead to the other universe. Kirby & friends investigate the doors by trying one of them out. Sonic and the gang investigate the doors to and entered one of them. Kirby's group ended up in Eggman's current Base and Sonic's group end up in ended up in Castle Dedede. After defeating the locations owners, both groups realize that their in another universe. Once they try to return to their home, they both fight against the other Universes sorcerrer (Kirby vs. Naugus, and Sonic vs. Marx). After the sorcerrers flee, both sides determine that they got a bad feeling this.
2- After a fight with the sorcerers, both Kirby's & Sonic's group figured out that their universe is merging with the other (as pointed out as various objects from the other universe showed up in their universe). Sonic's group went to Eggman's current base thinking that Eggman is involved with the merging, And Kirby's group go to the volcano to get the warp star back from a malfunctioning HR-D3. After Sonic and the gang defeated Eggman and his Egg Dragoon, they found out that Eggman is not causing the two universes to merge, but another powerfull surge that even the doctor can't figure out. After getting the warp star back, Kirby & friends place it back inside of Kabuu. Kabuu tells them that two powerfull entities are whats causing the merge, but couldn't tell who they are exactly. Meanwhile Sonic's group went ended up in Kabuu Canyon to see if the group they heard about are the "powerful surge". Both sides then meet and started to fight (with Kirby becoming Wheel Kirby to even the odds with Sonic). Then they stop after they see an unfinished Hallberd Mark II going to the other universe and the Blue Typhone ending up in the other.
3- The two ships have switched universes and start attacking the universe the ships there in. Both groups then realize their misunderstanding after realizing that they both have a common goal. Then they felt an earth quack after the realization. Tails & Tiff then concluded that the more the universes merge, both universes are going to get crumbled like a piece of paper. So they decide to take out the ships and find the real cause. Sonic, Tails, Knuckles, and Amy go to the Blue Typhone, Kirby, Tokkori, Tiff, and Tuff got the other universe and inside the Hallberd via the warp star. Sonic's group find the Ixis Naugus controling the Typhone from the control room. Kirby's group found Marx in the control room of the Hallberd and ended up in a fight with Kirby fighting alone. Sonic is fighting alone to, he keeps dodging Naugus' attacks while running after him. Eventually, both heroes managed to defeat their sorcerrer, but they manage to flee. But as soon as they exit the ships, they find that the universes are still merging. And they both ended up between the universes and find Marx and Naugus together right in front of them.
4 (final)- Both Kirby and Sonic's group said their sorcerrers name in surprise. Marx then explains how he ended up with Naugus. After his most recent defeat, he found himself drifting through the cosmos. He shortly encountered Ixis Naugus (who was in space longer than Marx), it was then that they learn that their from two different universes. And since Marx can't rule his universe, then he'll rule Naugus's. However Naugus wants the same thing, so they compromised to merge the universes together by combining their magic and make doors to travel freely while the universes are slowly merging (thus forming a team up). Tails and Tiff then warn them that the more the merging continues, the more damage they'll do to the universes. However they both didn't listen and declared that their going to crush Kirby & Sonic by merging together. They do so and became "Ixis Marx". Both teams realize that their homes will be destroyed as long as Ixis Marx is still around. The teams then form into one as they agree to find the chaos emeralds. Kirby goes off to find the warp star while the rest find the emeralds (in a similar fasion to the stage in the last story of Sonic 2006). Kirby then encounters Ixis Marx and distracts him by fighting him untill the group arrives. Ixis Marx then into the air and went into full power. The others arrive in time to see this, Kirby & Sonic then join forces. Kirby swallowed the warp star and got the star rod, Sonic used the power of the emeralds to become Super Sonic. Both Kirby and Super Sonic go battle Ixis Marx, with their own powers combined. After an intense battle, both heroes splitted Ixis Marx back to Naugus and Marx. Then they use their powers to stop the merging. Both teams then say their goodbyes and gave each other a souvenier (Kirby's team a dormant ring, Sonic's team a picture of Kirby's team). Kirby and Sonic then shake hands before they head back home. Kirby & friends end up back in the castle courtyard, Sonic's group end up back in Mobotropolis. Both sides then wonder if they will see each other again while looking at the sky.