To Baca's defense team, the former sheriff was a champion for transparency whose motive for restricting FBI access to the jails was to investigate what he had thought was a rogue operation that threatened jail safety.
The competing portrayals come to a jury after the U.S. Attorney's Office has already convicted seven deputies and former Undersheriff Paul Tanaka for obstruction of justice.
In previous trials, prosecutors labeled Tanaka as the mastermind. But on Wednesday, they called Baca the "driving force" and "the leader" in a conspiracy that stretched over a six-week period in 2011.
Prosecutor Brandon Fox chronicled a timeline to show Baca knew or should have known why the FBI had infiltrated the county jail. Over decades, reports of inmate abuse came from jail monitors and even a jail commander.
ACLU lawyers testified Wednesday that Baca listened to their complaints, but that the attacks continued.
"I don't think everything he said was insincere, but I think that he was warned and I think he knew and the reality was the total abuse and mistreatment of inmates continued," said ACLU Attorney Peter Eliasberg.
The FBI and the sheriff's department launched competing investigations as the FBI smuggled a contraband cellphone to inmate informant Anthony Brown so that he could notify them of inmate beatings. Deputies soon found the phone and its source.
Baca's defense said he was stonewalled when he went to the U.S. Attorney's Office for answers, explaining that inmates used cellphones to plot escapes, commit crimes and kill witnesses.
Baca said he was not in the loop about what deputies were doing regarding the actions of deputies attempting to hide an inmate informant and intimidate an FBI agent.
Baca, who had considered the FBI to be his partner in crime-fighting, blames the ordeal on rookie FBI agent Leah Marx, who led the investigation though she had no experience in undercover operations, nor in the jail system.
Baca said that he was following the wishes of the FBI assistant director to keep informant Brown, now uncovered as a "jail snitch" safe from retaliation.
Furthermore, Baca needed to know if there were other informants in the jail and more cellphones.
It led to a fiery exchange in a meeting with the FBI and U.S. Attorney Andre Birotte.
"I'm the goddamn sheriff - these are my goddamn jails," Baca told them.
Ultimately there was no ambiguity about which agency had legal authority to push forward.
Deputies sought a court order to compel the FBI to turn over its records. A superior court judge told them the court has no jurisdiction over any federal agency.