Sometimes prior to the events of Waluigi Unleashed, three separate apocalypses have befallen the Mushroom Kingdom and much of its former territory is divided among psychotic fiefdoms and para-millitary zones. One of them is ruled by an unseen, omnipotent Big Brother-esque figure know as the Overseer. The Overseer enforces its will using armed militias enhanced with performance-enhancing drugs and mind-controlled combat cyborgs, which he justifies in the name of rooting out subversive Primate Alliance agents. In response, several resistance movements have risen against the opression.
Waluigi is a member of the Overseer's military. Though questioning the Overseer's violent ways, he sees the leader as a source of order in a world of chaos.
Waluigi is assigned to assassinate Funky Kong, who is the leader of a guerrilla group aiming to annex Yo'Ster Island into a survivalist millitary state. After fighting through the guerilla troups, Waluigi corners Funky Kong, who simply states that "There are things you will never understand" and blows himself up with an Orange Grenade to avoid capture.
Before he can reach the extraction point, Waluigi and his squad are ambushed by members of another resistance group. The one behind the ambush, Bones, pities Waluigi and stuns him. He is taken to the resistance's HQ and briefied by sole surviving monarch Princess Daisy and chief engineer E.Gadd to be briefied on the resistance's goals and the Overseer's atrocities. Cornered and deprived of his morality-dulling drugs, Waluigi has no choice but to accept. Waluigi is then sent with a strike team to deactivate a military complex handling the anti-aircraft defense network surrounding the corporate regime's capital. During this sequence, Waluigi comes to face with an identical clone of his: Maluigi. The two blows and Waluigi come out victorious, but Maluigi escapes, vowing revenge.
At the resistance HQ, Daisy is consulting reports that the Overseer has nearly completed a deadly superweapon stored on the main floor of the presidential palace. Daisy decides to accelerates the timetable for the resistance's final assault despite Bones' pleas that they are not ready.
Waluigi is immediately relocated to the capital to participate in the assault. He fight through the streets and, during a lull in the action, is contacted by E.Gadd, who has been secretly dying of cancer and wants to be "absolved of his sins". The scientist reveals that Waluigi is, in fact, a clone with his memories genetically modificated; E.Gadd was the chief science officer of the Overseer's regime and handled the cloning process. Shocked by this development, Waluigi is temporally taken aback before deciding that is his "duty as an human being" to stop the Overseer. He then closes in on the presidential palace as reports reveal precisely what the secret superweapon is: A nuclear warhead (Codenamed: "Snufit Ball") that could cause a permanent nuclear winter should it be detonated.
Waluigi manages to reach the warhead's storage room, but it is guarded by Maluigi. The two fight to a stand-still, but Waluigi manages to convince his counterpart that he is understanding of his predicament (being a clone himself) and that they "can both live". Maluigi, touched by this display, offers to stay behind to deactivate the nuclear warhead. He successfully does so, at the cost of being lethally irradiated.
Waluigi fights to the Overseer's chamber. After a brief monolog, the Overseer reveals who he is: Wario. Losing his fortune and seeing all of his friend, including Waluigi, being killed during the Fourth Kremean War, Wario realized that the corrupt and decadent monarchies plunging the world into chaos could only be replaced by the strict efficiency of a corporate facscist rule. Wario transferred his brain into an inactive 80-feets exosuit to guarantee immortality and aims to bring the peace to the world, using an army of cloned super-soldiers based on Waluigi's DNA.
The clone Waluigi responds that he is insane and they fight. Waluigi is initially overpowered by Wario's powered armour body, but Rosalina appears to him in a vision and states that he is the "chosen one". Using his newfounds divine, he overpowers Wario's mechanical body and reluctantly destroy his brain.
Daisy contacts Waluigi by radio and congratulates him on his success, before offering him to be the recipient of a medal at the inauguration of the new monarchic government, but he tells her off. Daisy ask Waluigi who does he think he is, and Waluigi responds "I
AM
WALUIGI!".
At the beginning of Waluigi Unleashed II, Waluigi has retired from public view and lives as a rugged lumberjack in the backwoods of the radioactive Forest Kingdom. One night his place of residen is assaulted by a squad of mushroom kingdom spec-ops. After Waluigi use his advanced deducing skills to detemrine the spec-ops do not carry live round (in a sequence inspired by Rob Cohen's classic film xXx) Toad emerges from the shadows and explains that Waluigi's services are once again required: Primate Alliance cultists are attempting to create a bio-mechanical god.
Waluigi refuses, bu Toad explains that during his operation at the hand of the resistance, his body was stuffed with explosive nanobots which can be detonatd with a remote killswitch. Waluigi reluctantly accepts but insist he needs to form a "killer crew". For the purpose of the mission, Waluigi selects the notorious mercenary Oogtar, Lakitu (known for his "skills in genocide"), a cyborg Goomba named Goomborg, and John Freeman. Before investigating the cult proper, the team is tasked to board the international space station, taken over by Tiny Kong who uses it for ion strikes against civilian population centers.
The team heads to Koopa City to board the last surviving space shuttle launch pad. Once there, they find that the shuttle is guarded by Funky Kong, a sight that greatly distrubs Waluigi as he alredy killed him once. After Funky Kong once again ends his life with the cryptic words "There are things you will never understand", the soldiers board the space station. Fighting their way through it, they find Tiny Kong in the control room. Tiny Kong explains that the Primate Alliance goal's is to destroy all infrastructure modern society relies on to impose the Primate Alliance's strict millitary rule. The cultist are not part of the primate alliance, but rather an unrelated group supplied by it to hasten the collapse of the Mushroom Kingdom. The ape uses the opportunity to kill Goomborg and espaces with an espace pod the space station's as the self-destruct sequence is initiated.
Escaping the space station, Waluigi lands the space shuttle on the cult's purpose site of activity. As they reach the heart of the complex, Lakitu announces that he was a plant for the cultists and kill Oogtar. Waluigi is captured and taken before the cult's leader: Ashley. Having survived the Great Ape War, Ashley rejected witchcraft and embraced cybernetics. She expalins that the cultists are using ancient technology to create a boi-mechanical kaiju in the effige of Bowser, which will use its mind-control rays to bring the entire populace under their control.
Again empowered by a vision, Waluigi breaks free from his restraint and fights Ashley. Victorious, Waluigi throws her into the fusion core of the facility, destroying it. The resulting explosions causes an EMP wave that frys the killbots in Waluigi's body. No longer constrained to serve Toad, Waluigi departs the rubbles, looking for answer...