Pagano, 55, led Indianapolis to matching 11-5 records (though he was absent for part of 2012) in each of his first three seasons.
The coach reportedly turned down a one-year contract extension with a "modest" raise during the offseason, betting on himself heading into the final year of his contract, according to SportsCenter's Dianna Marie Russini. Rumors of tension between Pagano and general manager Ryan Grigson were persistent throughout the season, though both did their best to quell public speculation.
"We have no egos around here," Pagano told the Indianapolis Star (h/t Fox Sports) on Sept. 8. "Everybody checks them at the door every day they come to work. Players, coaches, myself, Ryan. The only thing that matters is the [horseshoe] and what's best for the 'shoe."
But those rumors only became more persistent after Indianapolis descended from Super Bowl contenders to a mediocre team.
A year after emerging among the NFL's best quarterbacks, Andrew Luck struggled badly with interceptions and lacked the same on-field demeanor. He was then limited to seven games because of injury, including a lacerated kidney that prematurely ended his season.
The Colts fanbase eventually fractured into camps siding with the coach or general manager.
Some looked at offseason acquisitions such as Gore and Johnson and wondered how Pagano couldn't coax a Super Bowl contender out of a team that had been one game away in 2014. Others pointed to the team's porous offensive line and wondered why Grigson did nothing to fix the problem after years of defenses pounding Luck in the pocket.
"That's been the case for three years now. Has it not? He should be more than comfortable dealing with what he's dealing with,” Pagano said of the pressure Luck faced after a Week 2 loss, per Gregg Doyel of the Indianapolis Star.
Irsay's decision to let Pagano stay is a surprising one, but clearly signifies the Colts owner trusts his head coach and believes the 2015 season was an anomaly.
Follow Tyler Conway (@jtylerconway) on Twitter.