Federal prosecutors are explaining why they have the gall to arrest and charge Don Lemon in connection with his coverage of an ICE protest that disrupted a Minnesota church service … they claim he wasn’t reporting from the sidelines, and was part of the plot to raid the church.

According to the federal indictment, obtained by TMZ, prosecutors allege Don conspired with protestors to “injure, oppress, threaten, and intimidate” clergy, staff, and congregants at Cities Church in Minneapolis.

The feds say Don met up with the protestors before the demonstration and got instructions on where they would be protesting and how the “operation” would go down once at the church.

Prosecutors say Don started livestreaming the morning of the Jan. 18 protest, telling his audience he was in Minnesota with an organization that was gearing up for a “resistance” operation against the federal government’s immigration policies.

The feds say Don took steps to “maintain operational secrecy” by not revealing the location of the planned protest to his audience … and prosecutors say he stepped away from a live mic so he “would not accidentally divulge certain portions of the planning session.”

On the way to the protest, prosecutors say Don told his livestream audience he needed to “catch up” to the demonstrators … and told his viewers, “We can’t say too much. We don’t want to give it up.”

Inside the church, the feds claim Don oppressed, threatened, and intimidated congregants and pastors just by being there … and during his livestream, they say he described congregants as frightened, scared, and crying, and told his audience the whole purpose of the protest was for it to be a traumatic and uncomfortable experience and to disrupt.

The feds say Don ignored the pastor’s request to leave the church … and they claim he confronted folks and obstructed them on their way out, challenging them about U.S. immigration policy.

Don, who previously told us he was there solely as a journalist, is charged with two federal crimes … one count of conspiracy against the right of religious freedom at a place of worship and one count of injuring, intimidating, and interfering with the exercise of the right of religious freedom at a place of worship.

As we reported … Don was arrested Thursday night in Los Angeles. His lawyer, Abbe Lowell, condemned the arrest and called it a distraction from the Renee Good and Alex Pretti killings in Minnesota.

Don’s attorney says he was simply exercising his First Amendment right as a reporter to document the church demonstration, shining a light on the truth and holding those in power accountable.

We told you all about it — the federal government sought to charge 8 people following the demonstration at Cities Church, including Don … but a magistrate did not approve charges against Don … leading the DOJ to go to a grand jury to secure an indictment against Don and 8 others.