Espionage, crime and politics collide in modern day Mexico City. A brilliant but self-destructive CIA officer, his young and ambitious Mexican-American protegee, and the city's inspirational but secretive Mayor all struggle for power during an invasion of the city by the world's most murderous drug cartel.

Isa recruits her first "asset," a source with connections to the cartel, but stretches ethical boundaries in the process. A visitor from Wayne's past dredges up unpleasant and violent memories. Lalo risks his relationship with his wife to pursue a rape prosecution against children of the rich and powerful. And Bautista’s plan for the city starts to become clearer.

Wayne, Isa and Pamela undertake a dangerous mission, infiltrating a corrupt banker who could lead them to the Guerrero cartel. Lalo and Isa start to bond while working on an art exhibition, but their past conflicts re-emerge to threaten their friendship. And Bautista’s sicarios conduct a mysterious operation that ends up having terrifying consequences for the city.

Wayne, Isa and Romero work frantically to rescue the hostages. Lalo and his police force do the same, but Lalo has his own agenda. Bautista carries out a mysterious plan involving his sicarios. And Wayne and Isa eventually come a terrible realization about why Bautista invaded the city.

Wayne's off-the-books operations finally catch up to him as Isa's fiancé pursues a lead that could put both Wayne and Isa in jail. Isa has to create a fake asset to cover up for Wayne’s misbehavior. Meanwhile, Bautista threatens Wayne’s life, but mysteriously, and ominously, lets him live. Veronica starts to realize the truth about her marriage. And Lalo gets his hands dirtier than ever before.

In the aftermath of the previous episode, Wayne, Isa, Veronica and Lalo all come to realizations about their lives and relationships. By the season’s end, the previous alliances have been destroyed and new ones are being built. And our main characters have to prepare for war, with new battle lines drawn.