The heroes remember what Fox had said and even goes into somewhat of a flashback. They then go back to the castle and talk to Professor E. Gadd. He then gave the heroes a Gameboy that is just like the old Emerald tracker but a new one. Mario then takes it and they leave as Princess Peach hopes they can save the world this time. The heroes then head to Donut Plains and look at where the Chaos Emerald is. They then spot a Chaos Emerald on the map and decide to split up. Luigi went with Yoshi and Mario, Sonic and Shadow went with one another.
Both teams then split up as Wario and Waluigi both go on a hunt to steal the heroes materials. Both teams are very lossed and seemed to not be able to find anything. A bunch of mishaps happen to the heroes when trying to find some of the Chaos Emeralds. Mario's team gets stuck in a Pipe Maze while Luigi and Yoshi both are fending off against creepy Mushroom World monsters like Goombas, Koopas and more. Luigi and Yoshi are dangling and then Luigi flips and gets eaten by a Pirahna Flower. Yoshi then uses his Flutter Kick to get Luigi. Luigi then decides to sit on Yoshi's back. Yoshi then carries Luigi as both hurry off to the end of the cliff. Meanwhile, Ganondorf senses a Chaos Emerald and heads towards it at tremendous speed. With nobody there to stop him, the heroes have to do something about it.
Mario's group get interrupted by Wario & Waluigi. Sonic demands they leave and get out the way but they just laugh. Shadow then threatens to kill them and They both then run for the hills. They then get lost in a Pipe Maze and turn back because of not finding the Chaos Emerald (assuming that Luigi and Yoshi found it). Luigi and Yoshi reach the end of the cliff and spot the Chaos Emerald. Yoshi then gets it and soon the edge of the cliff starts to fall. Both Luigi and Yoshi gasp and Luigi goes back to get Mario. Yoshi tries to get back up but falls. he then gets the Chaos Emerald again and is stopped by Ganondorf who demands for the Chaos Emerald. Yoshi gets stubborn and swallows the Chaos Emerald.
Ganondorf then prepares to attack as Yoshi turns into an egg. Ganondorf then kicks the egg and it keeps rolling. Ganondorf continuously keeps pounding the egg until it breaks and Yoshi gets punched to a wall. Ganondorf then punches Yoshi up and then kicks him down and uses his Cyclone Buster. Luigi crashes with Mario and tells them the news. They all then rush to the end of the cliff. Yoshi grabs Ganondorf with his tongue and then pushes him to the ground. Yoshi then throws eggs at him and then uses his Flutter Kick followed by another push to the ground. Ganondorf then underestimated him and quickly gets serious. Yoshi then gets hurt and gets swung by the tongue.
Yoshi then turns Ganondorf into an egg and gets ready to leave. Ganondorf gets out and then quickly Sky kicks Yoshi and then pounds him down. He then throws Yoshi up and then uses his Explosive Kick Wave. He then uses his ultimate attack and punches Yoshi. He then finishes Yoshi off with his Drop Kick. He does it again and retrieves the Chaos Emerald. Before Ganondorf boasts, the heroes arrive and he takes flight. They then see Yoshi and pray. They then start to head back to Mario's house where Princess Peach and Professor E. Gadd is waiting.