CHICAGO — Airlines were scrambling to accommodate travelers whose flights were canceled after a contract employee allegedly set fire at a suburban Chicago air traffic control center where he worked, halting flights at two of the nation’s busiest airports.

Brian Howard, 36, of Naperville, Ill., was charged Friday with destruction of aircraft or aircraft facilities, a felony. When paramedics found him, he was trying to cut his own throat, according to the criminal complaint. The FBI said Howard remains hospitalized and no court date has been scheduled.

The fire halted all traffic in and out of O’Hare and Midway airports. Delays and cancellations rippled through the air travel network from coast to coast after the fire. The ground stoppage at O’Hare and Midway raised questions about whether the Federal Aviation Administration has adequate backup plans to keep planes moving when a single facility has to shut down.

By Friday night, more than 2,000 flights in and out of Chicago had been canceled. Flights resumed after a five-hour gap, but planes were moving at a much-reduced pace, and no one could be sure when full service would be restored.

The FAA said in a statement Friday evening that it was managing the Aurora facility’s traffic through centers in Cleveland, Indianapolis, Kansas City and Minneapolis. The agency said it would continue working with those centers over the weekend to reduce disruptions.