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Elite Squad 2: The Enemy Within (Tropa de Elite 2: O Inimigo Agora é Outro)

Thirteen years after the events of the first film, BOPE Lieutenant Colonel (formerly Captain) Nascimento is ambushed while leaving a hospital. While his car is sprayed with bullets, his voiceover narrates the events leading to that point.

Four years prior, Nascimento arrives at Bangu Penitentiary Complex to quell a riot started by gangleader Beirada. Diogo Fraga, a teacher and human rights activist married to Nascimento's ex-wife Rosane, was sent to negotiate for a peaceful surrender. Fraga is escorted to the place and convinces Beirada to release the hostages, but Nascimento's protégé, Captain André Matias, shoots Beirada against Nascimento's orders, which results in multiple inmate deaths.

Nascimento learns that PMERJ commander Formoso plans to dismiss him due to the bad publicity and confronts him in a restaurant, only to be cheered by other diners for his tough line. Rio de Janeiro 's State Secretary for Public Safety Guaracy seizes the opportunity and promotes Nascimento as undersecretary, but transfers Matias back to the PMERJ as a scapegoat. Despite Nascimento's promises to help him, Matias speaks to journalist Clara Vidal about corruption in the government and lack of support to BOPE, leading to a month of jail and his estrangement from Nascimento. Meanwhile, Fraga is elected to Rio's State Assembly.

Through his new commanding position, Nascimento is able to expand BOPE's arsenal and personnel, granting it armored vehicles and a helicopter, which enables the force to eliminate entire drug cartels from favelas, in hope it will reduce police corruption. However, the absence of drug dealing as a controlling parallel power in these areas leads corrupt PMERJ Major Rocha and his men to form a police militia, ultimately taking over the community by extorting the inhabitants while also building a political machine, with support from the State Governor, Guaracy and Fortunato, a former television host now elected Representative for Rio.

Four years later, Rocha's militia has nearly taken over all of Western Rio. Disguised militiamen steal rifles from a police station in Tanque, one of the last drug dealing strongholds, providing their corrupt allies an excuse to authorize a police operation to expel the drug dealers (consequently clearing the way for the militia to take over). Nascimento listens to phonetaps of dealers and assures Guaracy they are uninvolved; however, corrupt Lieutenant-Colonel Fabio Barbosa claims an informant has implicated them and the raid is authorized. Matias, returned to BOPE by Rocha, occupies the station and ambushes the fleeing dealers, torturing captured drugleader Pepa to learn where the stolen weapons are. As Rocha arrives and inexplicably shoots Pepa, Matias confronts him, but is shot and killed by Rocha's men.

Devastated by Matias' death and aware Fraga has been investigating the militia, Nascimento taps his phone. Vidal, also investigating, enters one of Rocha's favelas and finds the Governor's re-election campaign material. She phones Fraga but is caught by Rocha's group, who kill her and her photographer. Nascimento listens to the call, realizes Fraga is now a target, takes the recording and goes after him; as he waits outside Fraga's building, Fraga, Rafael and Rosane arrive and are attacked in a drive-by shooting. Nascimento shoots the assailant, but Rafael is wounded. They take him to the hospital and Nascimento hands the recording to Fraga, whereupon he detains and assaults Guaracy, threatening to kill everyone involved if his son dies.

The Assembly opens an investigation into the journalists' disappearances based on the recording delivered by Fraga. However, Nascimento is accused of tapping Fraga's phone to spy on Rosane, forcing his resignation. Believing his militia will be scapegoats, Rocha attempts to ambush him after a visit to Rafael; however, Nascimento, expecting an attack, is aided by BOPE officers. They shoot some of the assailants, but Rocha escapes.

Nascimento is called to testify and implicates the Governor, Guaracy, Fortunato and many other individuals, as many of them are murdered to prevent them from testifying. The Governor, however, is re-elected and Guaracy becomes representative for Rio. The final scene shows Nascimento reflecting over the political scenario in Brazil and stating that "as long as the conditions for the system remain, it will remain". He visits Rafael as he slowly wakes from his coma.