Alonso denied that any challenges affected his decision to resign.
"The greater the challenges, the greater my commitment to stay in the district," he said. "I love that kind of adrenaline."
The facilities plan — which will build 15 new schools and renovate others — will be the bookend of the legacy of Alonso, whose earlier focus had been on leaving a formative mark on the culture of the district and solidifying its operations.
In 2008, Alonso introduced an initiative called "Fair Student Funding," which funded schools based on enrollment numbers and gave principals the autonomy to formulate their budgets around their priorities.
That year, the schools chief also sought to bring back dropouts, urging all high schools to place at least one phone call to students who had dropped out of school and visit their homes. By 2012, Alonso had cut the district's dropout rate in half.
In 2009, the district marked historic gains on state tests; emerged from "corrective action," in which the state was involved in the school system's governance because of poor test scores; and was celebrated by U.S. Department of Education Secretary Arne Duncan.
However, Alonso would later say cheating on test scores had taken place at the school Duncan visited, Abbottston Elementary. Flaws in the school system's cheating investigation, found by independent hearing officers, led to a reversal of his decision to fire the school's principal.
In 2009, Alonso's administration made its first public misstep, offering then-school board President Brian Morris a $175,000-a-year job as his deputy, only to find that he had a long history of financial and legal problems and hadn't finished his bachelor's degree at University of Maryland as he had claimed.
Alonso expanded school choice in 2010 to include middle and high school programs. By that year, the district had more than 30 charter schools and more than one dozen transformation programs that combine middle and high schools and include a college and/or career prep focus.
Alonso reached a landmark deal in October 2010 with the Baltimore Teachers Union that did away with traditional pay increases, and tied promotions and raises to student performance. The pact marked a stark contrast to October 2007, when teachers cast a vote of "no confidence" and picketed at headquarters to overthrow the schools chief and the school board when they came to an impasse on planning time during contract negotiations.
"We didn't always see eye-to-eye on all the issues, but we always managed to find a way to work together and find a solution that would best fit our teachers ... and students," Marietta English, president of the Baltimore Teachers Union, said in a statement. "The relationship between the BTU and management under Dr. Alonso should serve as an example of how collaboration works and how it can benefit all parties involved."
Melanie Hood-Wilson, chairwoman of the district's Parent and Community Advisory Board, said Alonso brought "tremendously positive change to our school system."
"While things are imperfect, the improvement has been substantial during his tenure as CEO," Hood-Wilson said in a statement. "He was unafraid to dismantle large portions of a very broken school system and build something that far better meets the needs of our kids."
Baltimore Sun reporter Yvonne Wenger contributed to this article.
•City schools CEO Andres Alonso will step down June 30.
•Alonso's current chief of staff, Tisha Edwards, will take over as interim CEO on July 1. She will be the interim CEO through the 2013-2014 school year.
•The city school board, whose members are jointly appointed by the mayor and the governor, will conduct an "exhaustive" national search for a new city schools CEO.e" national search for a new city schools CEO.