故事延續前作，當瑪利歐成功解救香菇王國公主，返回城堡後發現公主再次被過去的敵人壞利歐綁架。為了奪回城堡並打敗壞利歐，玩家需要收集六個金幣作為鑰匙，並與壞利歐進行最後一場決戰。這六個關卡包括：

1.《Tree Zone》：關卡內有許多巨大的樹木和昆蟲，最終頭目是一隻巨鳥。

2.《Space Zone》：充滿星星和月亮的關卡，最終頭目是外星人Tatanga，也是超級瑪利歐樂園一代的最終頭目。

3.《Macro Zone》：類似房屋的關卡，會將所有事物縮小，最終頭目是一隻水溝老鼠。

4.《Pumpkin Zone》：關卡位於巨人傑克的燈籠內，背景是墳墓和鬼屋，最終頭目是一隻老巫婆。

5.《Turtle Zone》：關卡位於一隻巨大龜內，最終頭目是躲在鯨魚內的章魚。

6.《Mario's Zone》：這是機械版的瑪利歐關卡，由三隻小豬看管。

最後一關就是瑪利歐城堡，成功收集六個金幣後，玩家將與壞利歐進行最後的決戰。

The story continues from the previous installment, where Mario successfully rescues Princess Toadstool of the Mushroom Kingdom. Upon returning to the castle, Mario discovers that the princess has once again been kidnapped by his old enemy, Wario. To reclaim the castle and defeat Wario, players must collect six coins as keys and engage in a final showdown with Wario. These six levels include:

1."Tree Zone": This level features numerous giant trees and insects, with the final boss being a giant bird.

2."Space Zone": A level filled with stars and moons, with the final boss being an alien named Tatanga, who is also the final boss of the original Super Mario Land.

3."Macro Zone": A house-like level that shrinks everything, with the final boss being a sewer rat.

4."Pumpkin Zone": This level is located inside the lantern of a giant named Jack, with a backdrop of graves and haunted houses, and the final boss being a witch.

5."Turtle Zone": Located inside a giant turtle, with the final boss being an octopus hiding inside a whale.

6."Mario's Zone": A mechanical version of Mario's level, overseen by three little pigs.

The final level is Mario's castle, where, after successfully collecting all six coins, players will engage in the ultimate showdown with Wario.