Yoshi fights the Gator Train from his own train, riding along next to him. At the start of the fight, the Shy Guys toss Spiked Balls onto Yoshi's train. After a while, the Gator Train tries to attack. He opens his mouth and thrusts toward Yoshi's train. However, this exposes his engine block. Firing an egg at his engine block damages him.
After the first hit, the Gator Train enters Phase 2. He rides by, releasing two Shy Guys. He then rams into Yoshi's train to derail the four passenger cars. Yoshi must get onto the next set, as falling onto the tracks will surely kill him. The Gator Train then gets back onto his own tracks to start Phase 3. However, ruler walls will appear to push Yoshi off the Yoshi train after the Shy Guys attack, so Yoshi must avoid their assault by jumping through the gaps. The Gator Train then performs his bite, leaving his engine exposed. Yoshi must then fire an egg towards the Gator Train's engine to damage him.
The Gator Train enters phase 4, which is basically phase 2 again. He then repeats his Shy Guy manoeuvre, with more balls. The Gator Train then fires coloured pencil skewers from his turrets. First, the pencils come from above, drilling their points onto Yoshi's train. Then, the pencils roll across the train. The Gator Train then repeats his bite attack, leaving his engine block exposed. Once Yoshi hits him a third time, the Gator Train is derailed, and Yoshi receives the pink Dream Gem.