From the start, Indianapolis Public Schools was reluctant to partner with Charter Schools USA.

Three years after state officials seized control of several academically struggling schools and chose outside charter managers, Indianapolis district leaders faced a choice: Were they willing to collaborate with the Florida-based company operating Emma Donnan Middle School in order to regain some oversight of the campus?

Indianapolis Public Schools, breaking its own policy against partnering with for-profit operators, agreed to work with Charter Schools USA. Together, they created a so-called innovation elementary school at Donnan.

The charter network had pitched this partnership to the state as a way for schools subject to a takeover to transition back to the district “without jeopardizing progress that has been made by the turnaround provider and without major disruption to the community.” Rather than a smooth transition, however, nearly five years of quiet partnership are ending with a dramatic breakup.

The IPS board voted unanimously Thursday not to renew its innovation agreement with the network, known as CSUSA, after little discussion.

“We gave it a chance,” said IPS board member Diane Arnold, who supported creating the partnership with CSUSA. “But I think it’s important for us to not let it go too far.”

Indianapolis Public Schools will now seek permission from the state board of education to take back control of Emma Donnan Middle School and choose a new manager for the campus. But the state board could instead decide to instruct CSUSA to pursue a charter to run the school independently — or to close the school altogether.

The IPS board decision comes just weeks before the Indiana Charter Schools Board is set to decide whether to grant charters to CSUSA to continue running Donnan and two other Indianapolis campuses — Howe and Manual high schools — that were also taken over by the state. The district’s last-minute play could hinder the charter network’s attempt to gain permanent control of all three campuses.

“Our board previously had said, ‘we’re not going to play a role,’ ” said Superintendent Aleesia Johnson of the IPS board at a media briefing Tuesday. “But the reality is, that’s 1,200 some odd students who are our students, who I believe we have a responsibility to.”

Johnson said her administration evaluated whether to renew the Donnan innovation contract with CSUSA independently from the other campuses. Still, the move is a clear sign that it is not likely to partner with CSUSA at Howe or Manual.

All three schools may be less financially sustainable without that alliance.

Officials from Charter Schools USA did not speak at either the Thursday meeting or Tuesday agenda review session the IPS board held. But in a statement Tuesday, a company spokeswoman, Colleen Reynolds, fired back at the district, accusing it of disrupting “students’ and teachers’ lives for political gain.”

“These actions do not deter us from our mission,” Reynolds wrote. “We have a proven track record showing tremendous improvement at all three schools over which we have managed and will continue to do so.”

The showdown marks the latest development in a political saga that began in 2012 when the academically struggling campuses were severed from the district by the state. The IPS superintendent at the time, Eugene White, went to war with Indiana education officials over the takeover, and the new operators accused the district of withholding student information and recruiting teens to transfer to other campuses.

The relationship changed, however, when former Superintendent Lewis Ferebee took the helm of Indianapolis Public Schools soon after and won over state policymakers. Indiana officials eventually returned Arlington High School, which had also been taken over, to local control. And under Ferebee’s administration, the district avoided state intervention by converting failing schools into innovation schools run by outside charter managers.

The district’s approach looks strikingly similar to the state’s decision years earlier to bring in Charter Schools USA. But, crucially, innovation partners are chosen by the district, which continues oversight, and managers are typically local.

“Having a partner who has history and connection to Indiana, to Indianapolis, is something that we have found the community values greatly and that we think makes for a more robust partnership,” Johnson said.

Reynolds, CSUSA’s spokeswoman, dismissed that argument, writing: “IPS has voiced concerns about local control without recognizing that local parents making a choice for their child’s education is the ultimate local control.”

Under Ferebee, Indianapolis Public Schools had largely abandoned any role in determining the future of Howe and Manual high schools. His 2017 plan for consolidating several other high schools, for example, called for closing Howe and Manual if they were returned to district control. And during a multi-month state process to determine the future of the three campuses, Indianapolis Public Schools did not offer plans to keep the schools open.

In March, Johnson made a last-minute request for the state board to delay its decision on the future of the schools while the district analyzed the financial implications of transferring the buildings to Charter School CSUSA. Johnson also raised the possibility that if the district regained control of Howe and Manual, it may keep them open as innovation schools.

The state board rebuffed the appeal for more time and instead instructed Charter Schools USA to seek charters to run the high schools independently of the district. The network has applied for charters for all three schools. But state officials expected that Donnan would continue as a K-8 innovation school under the district’s oversight.

Whether Indianapolis Public Schools is ultimately able to win back control of any of the schools hinges on the state, which is expected to consider the future of Donnan at its board meeting on December 4. If the state board backs Charter Schools USA, the network will also need charters to continue managing the schools. The State Charter Schools Board is expected to decide whether to grant charters to all three schools at a meeting on December 13.