The two will battle for the starting role this week.
"It's just a matter of the best man winning," Whittingham said.
Wynn badly wanted to be that guy this year after a third shoulder surgery, the second on his left arm. Unfortunately for the junior, a hit he suffered at the end of the second quarter in Friday's 27-20 overtime loss at Utah State was enough to knock him out of the game.
After consulting with his father and Whittingham, Wynn decided to call an end to his career.
It's likely he will have yet another surgery, according to Whittingham.
"He fought the good fight but enough is enough," the Utah coach said.
Wynn, who did not make himself available for media interviews, will remain with the team and assist Hays and Wilson this year.
The immediate need is to get them both ready to face BYU a week after the Utes played one of their worst games of the Whittingham era. Utah bounced back from a loss last year to beat the Cougars 54-10, but Whittingham noted that game was played under different circumstances.
"It was a different feeling," he said. "We went down to USC and played well and executed well for the most part. This week, it was complete shambles as far as how we executed."
If there was any consolation for the Utes, it is that Hays can't be blamed for much, if any, of the shambles.
The senior finished Friday's game 12 for 26 for 154 yards and a touchdown. The Utes were just 2 of 17 on third down conversions, but Hays wasn't the only one at fault since Utah didn't perform well in any phase of the game, Whittingham said.
The offensive line was porous in pass protection and the run game was ineffective. John White ran for 96 yards, but needed 27 carries, prompting Whittingham to call it a "complete stalemate."
So which guy gets to lead the Utes out of this mess? Hays has the upper hand based on experience, although it's a slim margin, Whittingham said.
"The gap is very small in practice and scrimmages," he said. "But you act differently when you are 'the guy.' Travis has been the supplemental guy. He has handled that role well, but it's different when you are 'the guy.'"
That Hays could be Utah's starter again normally would elicit groans from Utah fans everywhere, but he has improved immensely from a year ago and runs the offense with more command.
Following Friday's game, Hays said he was ready to lead the Utes.
"I feel good about this offense," he said. "I'll get with coach [Brian] Johnson and get ready for BYU, but I'm confident in this offense."
At 6-foot-6, 220 pounds, Wilson looks like a quarterback ready to play for a Pac-12 team. He just needs experience and will get plenty more in the future, Whittingham said.
"He has to take care of the football, not put it on the ground, not throw it to the other color and show complete command of the offense, and he has done all that," Whittingham said of Wilson. "There is nothing other than experience that he hasn't demonstrated."
And waiting in the wings in case of an emergency? Freshman Adam Schulz. The Muskego, Wis., native arrived at Utah as a walk-on, but earned a scholarship this summer.
Wynn's collegiate career started with such promise, with his rookie season culminating in an MVP performance in the Poinsettia Bowl win over California, but finished with injury milestones rather than achievements in his bio.
Utah's players hadn't heard of Wynn's decision before Monday afternoon, but none acted surprised.
"My heart goes out to him," tight end Dallin Rogers said. "It's a tough situation."
6-0, 208, Sr.
The good • Hays has experience running Utah's offense and was cool under pressure at Utah State.
The bad • While he is durable, Hays isn't as dangerous a runner as Wilson is.
The unknown • Hays has improved a lot since 2011, but has he improved enough to take Utah's offense where it needs to go?
6-6, 220, Fr.
The good • Wilson has very quick feet for a guy his size and also knows the offense relatively well since he participated in spring ball.
The bad • The majority of his snaps in games have resulted in handoffs. He did throw one 28-yard touchdown pass to Kenneth Scott Friday.
The unknown • Can he keep a cool head and run the offense efficiently in difficult situations?