CHICAGO — The Nets’ decision to rest Brook Lopez, Jeremy Lin and Trevor Booker in the final game of the season against the Bulls, who were in a three-team battle for the final two Eastern Conference playoff spots, was a case of the organization controlling what it can control without regard for any other team’s interests but their own.

Coach Kenny Atkinson explained before the Nets lost to the Bulls, 112-73, Wednesday night at United Center, the decision was made by he and general manager Sean Marks “in a vacuum” in terms of ignoring other factors, including the integrity of games that determine playoff berths.

“We’re looking out for the best for the Nets,” Atkinson said. “We want to go into this offseason healthy. It’s a huge offseason for us . . . When Sean and I talked, [it was about] what’s best for our franchise. We just took it in that vein and tried to leave the other stuff out.”

Feathers were ruffled in Miami, where the Heat began the night needing to defeat the Wizards and hoping either the Bulls lost to the Nets or the Pacers lost to the Hawks. The Heat won, but missed the playoffs when the Pacers also won. Jimmy Butler led the Bulls with 25 points, while Archie Goodwin’s 20 topped the Nets, who were plagued by 3-for-33 three-point shooting.

Describing his season-ending message to the Nets (20-62), Atkinson said, “I told them how much I appreciate their hard work and how they stuck together through tough times. We made a little progress, but we have a lot of work to do.”

Most of that progress was made over the 23 games before Wednesday night when Lin returned from injury and the Nets went 11-12. “You’d like to see the fruits of your labor start to show,” Atkinson said. “When we were stuck on nine [wins] for it seemed like forever, it seemed pretty dire. But when we were losing like that, we started to see the improvements . . . There was opportunity, and guys took advantage. Now, we need to take another step.”

Atkinson informed Lopez, Lin and Booker their seasons were over when the Nets arrived at their Chicago hotel on Tuesday. The previous night after a loss to the Celtics, Lopez said playing spoiler against twin brother Robin, who plays for the Bulls, was “like a dream.” But Wednesday, he accepted the Nets’ decision.

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Asked how he felt about missing the chance to face his brother in an important game, Lopez said, “I understand why they’re doing it of course. It’s frustrating for me. I wanted to be out there.

“But I think they just wanted to protect the two of us going into the offseason. It’s an important offseason obviously, and we’re looking to get a lot done.”

Lin missed 45 previous games primarily with hamstring injuries, but he said that wasn’t a factor. “As a competitor, I would love to play,” Lin said. “But I definitely understand why the organization wants to look out for me, and I appreciate that. Kenny talked to me, so, I understood where he was coming from.”

Lin’s absence Wednesday night had a glaring impact, but Goodwin rose to the occasion with 7-for-11 shooting and seven rebounds. “I guess my numbers were good, but I had five turnovers,” Goodwin said. “I got beat a couple times and gave up layups. That’s what I look at.”

Sounds like the Nets already are in offseason improvement mode.