Each and every Boston student should go to school in a building that’s safe, comfortable, and compatible with learning.

Getting there is the problem. The Boston Public Schools system — where two-thirds of the buildings were constructed before World War II — cannot get to the state of good repair its learners deserve without some pain and some disruption. BPS students and parents are now seeing the first wave of that pain.

The Walsh administration’s proposed school consolidation plan, BuildBPS,pairs new construction and some closures with a reconfiguration of grades so that most lower schools will go to grades 6 or 8 (many now are only K-5) and secondary schools will go from grades 7 or 9. Yes, it will be goodbye to the middle school.

The $1 billion 10-year construction program, launched in 2017, has now entered a critical phase. On the day that the city broke ground for the new Boston Arts Academy, it also announced plans to close at the end of this school year two high schools that now share the West Roxbury Education Complex — the Urban Science Academy and West Roxbury Academy — and the McCormack Middle School in Dorchester a year later.

The West Roxbury building, according to interim Superintendent Laura Perille, is in such bad shape it nearly wasn’t allowed to open for this school year after it failed an Inspectional Services Department review that cited a leaky roof and falling ceiling tiles. Emergency repairs are keeping the building together — for now.

How current West Roxbury students would be dispersed and whether a special program for students with autism could be kept together in a new location are among the issues causing anxiety in a process that has thus far lacked transparency.

But the fact remains that Boston is as long overdue for school closings as it is for new construction. An audit by McKinsey & Co., done at the request of the Walsh administration in 2015, found that BPS had roughly 93,000 seats for an enrollment of some 56,000 students. Using a different method of calculating “capacity,” the city today insists it has 69,100 seats for under 57,000 students but admits that middle schools are running at about 57 percent of capacity and vocational schools at 53 percent. And this in a system that has lost 8,000 students since 2000 alone.

Spare capacity means more money spent on maintenance, heat, and other costs unrelated to learning. So BuildBPS has to be not just about building newer and better, but building smarter and making the tough decisions about some schools that should not be replaced at all.

It is now no longer a mystery why Perille took herself out of the running for the permanent job of superintendent. She has now became the face of those tough decisions, announcing the first round of school closings — West Roxbury, which will be razed and rebuilt, and McCormick, which will be renovated as a new 7-12 high school. There are few jobs tougher than telling current students and their parents that things will get better — in a few years.

Release of this latest plan now sets the stage for community meetings — there was one on Tuesday in South Boston and there is another Thursday in Roxbury — and for some near-term decisions on those closures by the School Committee. But sadly it also sets the stage for conspiracy theories, and for neighbor vs. neighbor feuding about who gets what, when.

Still, nothing justifies keeping open a crumbling building. And empty seats in half-filled schools waste money that can be used on actual educational programming. If Boston is to be a city on the move, its public schools — newly reconfigured or newly built — must lead the way.