In late February 2009, Bart Scott followed his coach to New York. Rex Ryan had run his defense in Baltimore, and on February 27 Scott signed a six-year deal to play linebacker for him again, this time with the Jets.

He arrived with four straight 100-tackle seasons behind him and made it five in green. That first year the Jets finished first in the NFL in total defense, something the franchise had never done before. Over his first two seasons the club won 20 of 32 regular-season games and reached the AFC Championship Game in 2009 and again in 2010.

He played four seasons as a Jet, through 2012. The club released him on February 19, 2013, and later that year, after a total reconstruction of a big toe, he left the game.

Willie Colon came home in March 2013. He had spent seven seasons in Pittsburgh and won a Super Bowl XLIII ring there, and when the call came from Rex Ryan he did not stay on the market long. On March 15 he signed a one-year deal with the Jets.

His first fall in New York opened with three wins in five games, and in Week 6 the Jets met the Steelers at home, the team he had just left. On March 19, 2014, the Jets brought him back for another year at $2 million. That season ended at 4–12, and Ryan was out as coach.

Colon returned for a third year in 2015. In Week 8 against Oakland he hurt his knee, and 10 days later the Jets placed him on injured reserve. Hofstra Athletics counts 38 starts across his three seasons in New York. He retired in 2016.