The story begins with pure white. Suddenly, a hole with stars and planets expands in white, blank "room", and expanding faster and faster until the screen is filled with space.
We cut to a flash back of the original Space Crisis, back when the Primids were attacking. A Imperium fleet is heading towards Earth but is suddenly attacked by a mysterious monster that spits out blue flames.
The Imperium are destroyed by the monster, explaining their absence for the rest of the Space Crisis.
We then flash back to a lightning storm in space, where the USS Kelvin is investigating. The Narada, a Romulan ship attacks the USS Kelvin. Narada's first officer, Ayel, demands that the Kelvin's Captain Robau come aboard to negotiate a truce. Once aboard, Robau is questioned about an "Ambassador Spock", whom he professes not to know, and the current stardate. Narada's commander, Nero, kills him, and continues his attack on the Kelvin. George Kirk, the Kelvin's first officer, orders the ship's personnel, including his pregnant wife Winona, to evacuate the ship while he pilots the Kelvin on a collision course with the Narada. At the cost of his life, Kirk ensures Winona's survival, and she gives birth to their son, James T. Kirk.
CHAPTER ONE: THE FUSING
It cuts forward to the present time, in the Mushroom Kingdom where Mario and Luigi find themselves alive again. They find that not only is their universe whole again but that most of the Mushroom Kingdom enemies have fused with each other.
Mario and Luigi meet up with Sonic and Tails, who tell them the fused creatures are in their location as well. They then meet Ganondorf, who tells them that he is working with the Fusionist, who not only fused their dimensions together again but is planning to take over it as a cohesive whole and that he has asked Ganondorf to take out some of the heroes to fuse together as one of his minions. Mario and the other fight Ganondorf and he soon disappears into the shadow.
R.O.B discovers that the floating island where his people lived is some how back, and he decides to lead his people again.
Touko finds the labatory and goes up against Scientist Nathan. Once he looses, he releases Genesect, who proceeds to attack Nathan and then attack Touko.
After defeating Genesect and turning it into a trophy, Touko attempts to capture it but the trophy is taken by Yzma and Kronk. Touko sends out her Pokemon to chase them down.
A strange ship proceeds to let Yzma and Kronk inside, and Touko's pokemon are locked out and can only watch as the strange ship flies away.
Ness hears a loud sound come from outside. After going to crash site on top of the hill, it turns out to be Zim's ship. Ness proceeds to fight Zim.
Zim is defeated and turned into a trophy, but not before Dib takes it for himself. Dib jumps down the hill and Ness proceeds to walk home.