Air traffic controllers took to the picket lines including Thornton, he and several others were arrested and charged with felony counts. Thornton was held for ten days at the Fairfax County, Virginia jail. “John paid the ultimate sacrifice in 1981 so he could better the profession and workplace for future generations of air traffic controllers,” said National Air Traffic Controllers Association (NATCA) Executive Vice President Trish Gilbert.

As with many air traffic controllers Thornton loss his job and began selling life insurance. In 1983, "air traffic controllers looking to organize a new union sought Thornton’s help. Despite the pain and damage of the walkout, Thornton overcame his emotions and accepted the offer, immersing himself in a nationwide effort that culminated with a new union with new goals - NATCA".

During the years to follow Thornton played a major role in the reorganizing and shaping of a labor union that air traffic controllers could proudly vote for. Thornton persuaded the Marine Engineers' Beneficial Association (M.E.B.A.), the oldest maritime trade union in the United States and a member of the AFL–CIO, to let him go on the road as a national organizing coordinator.  This was a very difficult time for air traffic controllers as well the aviation industry.

On June 11, 1987, over 70 percent of the air traffic controllers voted in favor of NATCA as their sole bargaining union. Thornton said, "I'd like to say it was smart organizing on my part, but it may just have been that we were the only remedy available." On June 19 the FLRA certified NATCA as the air traffic controllers union. Thornton served at NATCA as the interim president until July 18, 1988, when NATCA elected Steve Bell as their first president and Ray Spickler their Executive Vice President. At which time Thornton was appointed as NATCA’s senior director of legislative affairs, a position he served in for seven years. Thornton served for more than 10 years with NATCA until 1995. He served as the unions’ national coordinator, executive director and senior director of legislative affairs and a number of executive positions.

Thornton told the Los Angeles Times in June 1987, "We want a non-adversarial relationship with the FAA Not a lot of rhetoric. Not a lot of confrontation. If we went out and started condemning them, got that old antagonism going again, we really couldn't expect them to say, 'OK, we'll deal with you in a upright manner." On July 23, 1987, Thornton spoke before the Aviation Safety Commission on his concerns with safety and work conditions at the FAA. “The Controllers who voted for NATCA are extremely concerned by the deteriorating margin of safety in the Air Traffic Control System and the lack of corrective action by the FAA. They believe that a union can make a difference, in air safety where they as individuals could not. That is why we are appearing before you today."