The indictment follows an investigation conducted by the FBI.
The slain 24-year-old, Anthony Lamar Smith, was shot five times by Stockley. Police recovered a gun from Smith's car, but found only Stockley's DNA on it, leading many to believe that the firearm was planted.
One hundred and forty people were mass arrested on October 3, 2017, after Stockley was found not guilty on charges of first-degree murder. The group included protesters, reporters and an undercover police officer.
Protests were held in the city for days surrounding the verdict.
The officer, named in the indictment as "L.H.," had been in the department for 22 years before he was allegedly subjected to excessive force at the hands of officers Dustin Boone, Bailey Colletta, Randy Hays and Christopher Myers.
"While these officers have been indicted for illegally abusing an undercover officer they mistook for a protester, there has still been no real accountability for the individual officers who engaged in the same behavior toward protesters," ACLU of Missouri Legal Director Tony Rothert said.
The officers have been suspended without pay. Some 91 cases involving the four officers have been dismissed, and local prosecutors are reviewing even more for possible dismissal.
The officers face charges of excessive force over their use of dangerous weapons and conspiracy to obstruct justice. Three of the officers are also accused of throwing their undercover colleague on the ground before kicking and striking him, as well as attempting to destroy his cell phone.
Officer Colletta, who was dating Officer Hays, is accused of lying to the FBI when she told him that the undercover officer was "brought to the ground very gently." In fact, she knew he was slammed down, according to the indictment.
That night of the protest, St. Louis Police's Civil Disobedience Team — charged with handling protests — was told to control "the crowd as needed and arresting those individuals from whom there was probable cause to believe that they had committed crimes," according to the Department of Justice. Nonetheless, police wound up surrounding a large group of protesters in a tactic referred to as "kettling" before arresting all of them.
Officers mocked the demonstrators by appropriating the popular protest chant "Whose streets? Our streets!" while they were detaining them.
"Let's go whoop some ass," Officer Myers wrote in a text message to an unknown person that day.
"The more the merrier!!! It's gonna get IGNORANT tonight!! But it's gonna be a lot of fun beating the hell out of these shitheads once the sun goes down and nobody can tell us apart!!!!" Officer Boone wrote. "We really need these fuckers to start acting up so we can have some fun."
Protests against the ruling in the Stockley case went on nightly for weeks, starting on September 15, 2017. "I'm still enjoying each night," Officer Boone wrote on September 17 of that year.
The excessive force charge, which three of the officers face, could land them in prison for 10 years, but all defendants could face 20 years if they are found guilty of obstructing justice. They could also receive fines up to $250,000 each.