In the fictional metropolis of Champion City, a trio of amateur superheroes is on a quest to make a name for themselves. Among them are Roy (known as Mr. Furious) portrayed by Ben Stiller, Eddie aka The Shoveler played by William H. Macy, and Jeffery who takes on the role of The Blue Raja. Each possesses unique abilities: Mr. Furious harnesses his rage to boost his strength and agility, The Shoveler employs a shovel as his weapon of choice while showcasing his superhuman agility, and The Blue Raja boasts an extraordinary knack for throwing projectiles with superhuman accuracy.
Despite their ambitions, the trio constantly faces setbacks due to their lack of experience and unresolved conflicts among themselves. Their attempts often lead to situations where they are outshined by their more famous counterpart, Lance Hunt (alias Captain Amazing), depicted by Greg Kinnear. Captain Amazing finds himself in precarious waters as he realizes that his ability to capture every villain has rendered Champion City almost crime-free, putting his corporate sponsorship at risk. Desperate to revive his career, he conspires to unleash the notorious super-villain Casanova Frankenstein, played by Geoffrey Rush, with the help of his benevolent psychiatrist Dr. Anabel Leek (Lena Olin), who harbors a secret affection for her patient.
Eddie’s devoted wife, Lucille (Jenifer Lewis), supports her husband’s super aspirations even after twelve long years of his pursuit, urging him to prioritize family over fantasy. Meanwhile, Jeffery lives with his mother Violet (Louise Lasser), and Roy scrapes by working in a junkyard. Unfortunately, their plans spiral out of control as Casanova escapes his confinement, alongside his cohorts known as the Disco Boys, eventually capturing Captain Amazing and plotting to construct a reality-altering weapon named the "Psycho-Frakulator."
As events unfold, Mr. Furious learns of Captain Amazing's capture and rallies his friends. They charge into action but quickly find themselves outmatched by the Disco Boys. Realizing they require additional support, they recruit quirky sidekicks like The Spleen (Paul Reubens), who can incapacitate foes with his flatulence, Invisible Boy (Kel Mitchell) who can only turn invisible when no one is looking, and The Bowler, played by Janeane Garofalo, a superhero equipped with psychic powers that channel the spirit of her deceased father through her crystal bowling ball.
Their attempts to confront Casanova are initially met with failure, annoying him instead of making an impact. During a moment of crisis, they encounter the enigmatic Sphinx (Wes Studi), a seasoned superhero who attempts to instill discipline and teamwork within the group through tedious training exercises. This frustrates Mr. Furious, leading him to temporarily abandon the team. However, they soon realize the infusion of weaponry via the mad scientist Dr. Heller (Tom Waits) significantly enhances their potential with innovative gadgets.
Reinvigorated by a relationship with Monica (Claire Forlani), Mr. Furious returns to battle alongside his teammates. They storm Casanova's lair during a gathering of city gangs, but chaos ensues when their adversaries accidentally activate the Psycho-Frakulator, leading to dire consequences for Captain Amazing.
As despair looms over the team due to Captain Amazing's absence, a powerful pep talk from The Shoveler reignites their spirits, propelling them back into action. Utilizing their quirky powers, they overcome henchmen and push through to confront Casanova. In a pivotal showdown, Mr. Furious finally taps into his inner rage and gains an upper hand, defeating Casanova, who meets his demise at the hands of the Psycho-Frakulator.
With the villain vanquished and the Psycho-Frakulator destroyed, the team escapes, but not without a humorous aftermath: reporters swarm them, inquiring about their superhero name. As they argue amongst themselves, one reporter exclaims, "Well, whoever they are, Champion City owes a great debt of gratitude to these 'Mystery Men,'" highlighting the comedic chaos and disarray that define their journey.
