El Mariachi, played by Antonio Banderas, is enlisted by CIA officer Johnny Depp as a hitman to eliminate General Emiliano Marquez, a corrupt figure within the Mexican Army. Marquez is in league with drug lord Willem Dafoe, who has sinister plans to assassinate the President of Mexico during a time of turmoil in Culiacan, the capital of Sinaloa. The President, who is keenly aware of this threat, calls upon the citizens of Culiacan to band together and resist Barillo's attempts to destabilize their country.
Nicholas, the President's advisor, shares that Barillo enjoys a folk-hero status in Culiacan, having acquired large swathes of land for the people. However, the President counters that the townsfolk are aware of Barillo's true nature as a mass murderer and believes in their ability to discern the truth. Confident in the resolve of his people, he rallies them to defend what is just.
Sands connects with El Mariachi through his agent, Cucuy, fully aware that antagonistic cartels desire to assassinate him. Concurrently, Barillo has devised a deceptive plan to carry out facial reconstruction surgery on an accomplice, allowing the lookalike to assume his identity.
Belini, portrayed by Cheech Marin, recounts El Mariachi's tragic past involving his wife, Salma Hayek. Years ago, El Mariachi, then a simple musician, engaged in a fierce standoff with Marquez. Their lives intertwined dramatically when Carolina betrayed Marquez and united with El Mariachi, severing her past ties. However, vengeance marked their story when Marquez retaliated against the couple, leading to a gruesome ambush that took the lives of Carolina and their child. This deep-seated enmity drives El Mariachi to avenge his family's murder.
Sands offers Belini a handsome sum for El Mariachi's details, which eventually leads to them meeting in a church. Here, El Mariachi faces a brutal attack from hitmen sent by Sands as a test of his skills. Sands also persuades retired FBI agent Jorge Ramirez to hunt down Barillo, who killed his partner, Archuleta, after torturing him. As Ramirez embarks on this path, he finds an unlikely ally in Billy Chambers, an American fugitive disillusioned by Barillo's dreadful reign.
While monitoring Barillo, Ramirez encounters Ajedrez, a competent operative with her own struggles for recognition, as local authorities dismiss her capabilities due to her gender. Sands, however, is single-minded in his goal to eliminate the President while ensuring Marquez meets his end, believing it will help Mexico find its way back to stability. Meanwhile, Cucuy betrays El Mariachi by handing him over to Barillo, but the tables turn when El Mariachi escapes.
In a harrowing turn of events, the chaos escalates during the Day of the Dead celebrations as Marquez attacks the presidential palace. Despite Sands' instructions, the Mariachis spring into action to protect the President, believing in his integrity. El Mariachi confronts Marquez once more, delivering lethal justice by shooting him in the knees and then finishing him with a clear shot to the head.
As the dust settles, Ramirez kills Barillo, who has been responsible for so much pain, while Sands manages to dispatch Ajedrez, reclaiming hope for the future. Lorenzo and Fideo, friends of El Mariachi, take the opportunity to pocket Barillo's funds. As peace begins to restore, Ramirez finally avenges his partner's demise, and El Mariachi generously donates his share of the bounty to his village before embarking on a hopeful journey into the sunset.
