King Lerna, enraged by his defeat by Coyo, plans to get revenge and wipe out Coyo - along with Cammy Isles to prove his worth. Attempting to ensure his victory, he joins allegiance with the inhabitants of Iggy Isles...an ancient and peaceful tribe, however they become enraged when the Ig-Ig Charm is stolen from them, which Lerna blames the Cammy Isles on (Though he stole it himself). The Ig-Ig Charm was the only thing keeping the terrifying Kojira at bay. Kojira once ruled over Iggy Isles as a hulking monster, but his power was stripped from him and sealed in the Ig-Ig Charm...and now with the Charm removed, Kojira will be released.
After these events, the peaceful Cammy Isles are invaded by the Iggy Islanders and their leader, a prince named Igoo. They steal the Cam-Cam Charm and give the 7 peaces to Lerna's subordinates, and learning of this, Coyo sets out to retrieve them and stop Lerna.
The Legend of Coyo II stays truthful to the original, adding mechanics of course. Coyo keeps his main moves, Tropicannons, and Healing Items along the adventure, but some new objects make it into the picture.
Power Charms are added, which are types of power-ups located everywhere, these powerups can be found by ruffling bushes or by beating enemies (who will have a rare chance to drop them). These power-ups include: The Pineapple Launcher, which will launch powerful pineapples at enemies - killing them, The Camo Cap, which when worn will make Coyo camouflage with the background while moving, which will make enemies ignore him (He can still get hurt, however), and The Cupido Wings, which will allow Coyo to fly. There's also the Magi-Magi Charm, which will allow Coyo to absorb the charm, and fly at high speeds while invincible, it will wear off after a bit.
The Legend of Coyo II keeps all of it's old modes, also including the Superstar Mode (Unlocked after beating Story Mode 100%). This mode is for players who want a challenge, and has you going through the entire game with 10 health on the HP Meter (contrary to the normal 30), takes away all extra 1-Ups, and ups the AI difficulty on the bosses. There's also the Theater Mode, unlocked after beating Story Mode at any percent, this mode lets you listen to all the music tracks and watch all the cutscenes in the game.
- King Kibble's Revenge (Fought at Saganage Forest)
- Wolfur (Fought at Moon Plains)
- Snow-Mon (Fought at Wintaria)
- Sharca (Fought at Copper Sea)
- Volcalona (Fought at Mt. Blister)
- King Lerna (Fought at Lernia)
- Prince Igoo (Fought at Iggy Isles) / Eyezer (Secret Boss)
- Kojira (Fought at Kojira's Keep)