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SANTA CLARA — Less than 24 hours after NaVorro Bowman requested his release, the 49ers granted it on Friday, and now the legendary linebacker is a free agent.

The 49ers had benched Bowman, 29, for a few drives during their overtime loss to the Colts last Sunday. After the game, Bowman was upset with the coaches and said he didn’t understand their decision to take him out of the game.

“They’re going to do what they want to do,” Bowman said. “I don’t know. I don’t like it. No one likes coming out of the game, but I’m a team player.”

Head coach Kyle Shanahan told the media the 49ers wanted to keep Bowman fresh to give him his best chance to play well, and that’s why they took him out of Sunday’s game. Bowman tore his Achilles tendon last October, which followed severe injuries to his knee in 2014. Shanahan said he would continue to rest Bowman for a couple drives every game moving forward.

On Monday, Bowman’s agent, Drew Rosenhaus, called 49ers general manager John Lynch to tell him Bowman didn’t like that plan.

“I told (Rosenhaus),” Lynch said Friday afternoon in the 49ers auditorium, “that I had talked to Kyle and his staff and that we were convinced that we felt this was the best thing for (Bowman). In response, Drew communicated that if that’s the case, NaVorro would prefer to be traded.”

The 49ers didn’t try to trade Bowman right away.

“We kind of let everyone cool down there for a day or so,” Lynch said. Then, on Thursday after practice, Lynch and Shanahan met with Bowman face to face.

“Since then,” Lynch said, “we’ve been working in earnest to find a trade partner. We had a couple teams that were very interested, came very close to happening. Ultimately, we were working with NaVorro and his representation to try to get this thing across the finish line.

“We felt like NaVorro had earned the right to have some options and some choices that he deemed the right ones for him. In the end, he chose that he would rather look at all 31 teams, and we granted his request (to be released).”

Shanahan then explained the basis of the disagreement between him and Bowman.

“NaVorro was right at the top in terms of reps as any linebacker in this league. And the scheme that we play — being a little bit different than what he has done in the past — he’s got to run a lot more, got to cover a lot more ground. I thought it would help Bo out to play at a higher level if we took him out a couple series throughout a game. I thought it would save his legs more, give him the energy and burst he needed to play in this scheme. And he respectfully disagreed.”

The 49ers tried to trade Bowman during May, according to former NFL GM and current contributor to “The Ringer,” Michael Lombardi. The 49ers denied this report.

Throughout offseason practices, Bowman struggled moving and changing directions, especially during pass coverage. He couldn’t cover one of the slowest players on the 49ers offense — tight end Garrett Celek. This led to speculation the 49ers might release Bowman before the season began, but they did not.

“We weren’t ready to yet,” Lynch said. “Bowman was coming off an injury, and you just don’t know how that’s going to go. So, we wanted to see where he could get in terms of how effective he could be. We felt like he made us better at the time. Now, we feel this is in the best interest (of the 49ers).”

Bowman’s struggles became particularly apparent in Week 3 when the 49ers played the Rams. Bowman missed six tackles and repeatedly slipped and fell when he tried to change directions.

The next week, Bowman had trouble planting his foot and driving forward during pass coverage, and gave up two critical completions to running back Andre Ellington during the 49ers’ overtime loss to the Cardinals.

“You don’t anticipate two checkdowns getting a combined 20 yards,” 49ers defensive coordinator Robert Saleh said a few days after that game. “That’s bad ball, very bad ball, to be honest with you.”

Presumably, the coaches blamed Bowman for Ellington’s long gains. So, they came up with the plan to reduce Bowman’s playing time: Maybe he would play better during crunchtime if he wasn’t tired.

But that plan didn’t work. Even early in the game against the Colts, Bowman looked slow, failing more than once to run down ballcarriers near the sideline. His Achilles injury clearly has diminished his speed, quickness and agility. He may never be a dominant player again.

Rookie Reuben Foster will replace Bowman as the 49ers’ middle linebacker. Bowman had a distinguished career with 709 tackles for San Francisco, where he played seven seasons, making the All-Pro team four times.

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