One morning while Wario is sleeping in his castle, Captain Syrup and her Black Sugar Gang sneak into his home. The invaders manage to steal all of Wario's treasure he had collected in the first Wario Land game and flood his home by leaving a large water faucet in his basement running. During the raid, the Pirate Gooms accidentally set off Wario's giant alarm clock, but make their escape before he begins stirring. Eventually Wario wakes up and figures out what Syrup and her Gooms have done, setting out to find them. He pursues the Brown Sugar Gang across the varied areas outside of his castle in the hopes of having his treasure returned and gaining his revenge against the intruders.
Wario Land 2 is noticeably different from the first Wario Land game. The most notable difference is that Wario is now invulnerable, and is instead susceptible to different effects from enemy effects. For instance if an enemy stomps on Wario's head, he might be flattened, enabling him to cross gaps he might otherwise have fallen through. Of course some enemies are just nuisances and won't help Wario in any way, but regardless an enemy will never cause Wario to die. This change emphasizes puzzle solving and platforming rather than traditional survival.
The game has several branching level paths that change how the game's storyline plays out, many of which have their own variation of the game's ending. Once the player has completed one of the endings, they can select any stage they have completed and see which treasures they have and have not collected. In order to see the game's "true" ending, the player has to collect every treasure available in the game and complete the entire picture panel that appears after a level is completed.
Each world, or chapter, consists of five stages and one boss (usually). With only 25 of 50 stages being available with the standard playthrough, searching for hidden level exits adds to the replayability of the game.
Chapter 1: One Noisy Morning
The first chapter takes place in Wario's castle and dungeon, kicking out his invaders and doing some damage control. Basic gameplay mechanics are introduced. The very first level also features the most fiendishly hidden secret level exit in the game.
Chapter 2: SS Tea Cup
Chapter 2 features the outskirts of Wario's Castle and a return to Captain Syrup's flagship, the SS Tea Cup. This chapter includes an escort mission, of sorts, involving Wario's prize hen, and water/nautical themed levels. The boss of the chapter is Bobo, also familiar from Wario Land 1.
Chapter 3: Maze Woods
A heavily forested area, several of the Maze Woods levels are arguably the most punitive, requiring above average reaction skills from the player. The Puffy Wario form is introduced, as is flying by owl.
Chapter 4: In Town
An urban themed environment, complete with breaking-and-entering shenanigans! Culminates in a basketball showdown with a giant rabbit, of all things.
Chapter 5: Syrup Castle
As the (ordinarily) final chapter, the completely rebuilt Syrup Castle is another castle environment filled with traps and hidden areas. Tricky platforming a puzzles abound, but you can finally confront Captain Syrup and her floating bomb deployment platform in an elaborate multi-stage fight! Well, okay, two stages. Requiring 2 hits each. Still, with her defeat Wario can demolish Syrup's tower a second time, and reclaim his stolen loot.
Secret Chapter 1: Invade Wario Castle
As mentioned, the entrance to the very first secret chapter is fiendishly hidden, and nearly impossible to intentionally reach. Hidden in the first level of the game, you must simply... do nothing. As Wario starts off asleep, simply refraining from touching any buttons will leave him in his slumber, ending the level soon after. In this alternate route, Wario was never awakened by his alarm clock, and Syrup's gang simply toss Wario out and move in! This exit is not reachable the first time you play the game, and can only be accessed after you beat it once, possibly adding to the confusion. The chapter is heavy on the castle theme, as ends with a showdown with Syrup and an armor-plated, radio controlled, robotic giant spear man.
Secret Chapter 2: Go To The Cellar
In this alternate route, following the first chapter, Wario takes a short-cut to Maze Woods through the dungeons and caves beneath his castle, meaning the levels are subterranean in theme. Most of these levels are filled with underground monsters and ghosts, although one does take place on a train very similar to the one Wario travels on during the "In Town" chapter. The area's final boss is a repeat of a fight which took place in the original Wario Land, which pits Wario against a giant bull who wants to knock him off of a platform.
Secret Chapter 3: Ruins At the Bottom of the Sea
If Wario stumbles upon the giant cork blocking a leak in the SS Tea Cup, he may destroy it, sinking the ship with all hands. Luckily, they are able to emerge in a series of ancient underwater ruins filled with ancient traps and ancient treasure, and so on. The chapter diverges at the fourth level, allowing Wario to continue down the standard path again or go on to the fifth level, containing a game-end boss. This time, Syrup has been captured by a nefarious self-inflatable newt, whose behind Wario kicks, along with Syrup, for good measure.
Secret Chapter 4: Mysterious Factory
Accessible from the factory level in Town, Wario follows Syrup into her hideout in a seemingly purposeless and highly dangerous industrial complex. Get ready for some intense conveyor belt action!
Secret Chapter 5: Uncanny Mansion
Also an alternate route from Town, Wario tracks Syrup down in a spooky haunted mansion, filled with a number of devilish puzzles and challenges. The end boss is a slimy ghost with Syrup in his clutches. After defeating him, Wario spots his stolen treasure, but falls down a hidden trap door! Seemingly endless, Wario keeps falling until, (phew!) he wakes up in his bed. It was all a dream! And in a twist on the usual credits sequence, which shows Wario running home with his treasure, we are shown a hot air balloon with Syrup's insignia flying to Wario's castle. Looks like the dream came true.
The Really Final Chapter: Steal the Syrup Treasure!
Collecting every single treasure and map piece unlocks the true final level: Syrup's treasure vault! A bizarre and surreal environment, this time challenge level tests every skill you've learned and introduces a couple new ones in this challenging and worthy final stage. As it turns out, the final boss is... the giant spear man. Last line of defense or the puppet master? We may never know.
While Wario may be invincible this time around, Wario Land 2 introduces many transformations that change Wario's abilities. Often the player must use these temporary forms to solve platforming challenges, or avoid gaining them to pass a room.
After being force-fed cake by rogue chefs, Wario swells to an impressive size. His speed and jumping is severely restricted, but he now breaks blocks by simply jumping onto them, and crushes enemies underfoot.
Being flattened by a stone idol turns Wario comically flat. He becomes defenseless but can lazily drift through the air like a sheet of paper, allowing him to cross chasms and fit into small gaps, as well as crossing holes in the floor he would otherwise fall through.
Wario is highly allergic to bee stings! Being stung makes Wario's face puff up and apparently fill with helium, causing him to float to the ceiling.
Being hit by a hammer turns Wario into a human spring, turning him defenseless but allowing him to jump much higher.
Touching a ghost or being infected by a fellow zombie turns Wario undead. He loses the ability to jump, but can now fall through thin floors.