Kelly arrived in Eugene as the offensive coordinator in 2007 as almost a complete unknown, but the former New Hampshire assistant's no-huddle spread option offense would instantly propel quarterback Dennis Dixon to Heisman Trophy frontrunner and Oregon to BCS championship favorite before Dixon's season-ending knee injury.
In the blink of an eye, Kelly would succeed Mike Bellotti as head coach and take Oregon to four BCS bowls in his four seasons at the helm, including its first Rose Bowl win since 1917, three Pac-10/12 championships, and a 46-7 record.
Now Kelly is gone, days after it seemed like he would stay at Oregon for another season after his initial flirtation with the Philadelphia Eagles went nowhere, with offensive coordinator Mark Helfrich expected to be promoted to the top job.
But don't expect Oregon to suddenly disappear from the national scene and Pac-12 prominence, anytime soon at least. If anything, Kelly's exit quickly increases the pressure on opponents in the conference, while giving Oregon the added advantage of somewhat reduced expectations heading into 2013.
No one really knows how lines of succession will work out, especially given the unique essence of Kelly's offense. This has been his vision, tweaking its exact nature to match the varying skills of his quarterbacks. And while players have expressed their admiration for Helfrich and there were more stories this season about his role in putting together the game plan, Kelly called the plays.
However, Helfrich inherits a core group including quarterback Marcus Mariota, running back De'Anthony Thomas, and center Hroniss Grasu that is extremely well versed in the offense. They will know how to keep the system working, much as the experience and physical skills of the 2005 USC offense managed to overcome the interference of Lane Kiffin and Steve Sarkisian after the loss of offensive coordinator Norm Chow.
They also have a schedule that is more than conducive to another run to the BCS championship game.
That will be overlooked, however. History says Helfrich's Oregon will be undervalued and underestimated in the preseason polls, much in the same way Stanford was in David Shaw's first season two years ago.
The Cardinal now looks to be a solid favorite to win the Pac-12, as opposed to a true toss-up coming into the day. Washington, seeking to take a step forward, must now feel like it has at least a chance to compete with Oregon after being continually manhandled by Kelly's team. So too must UCLA, which avoided Oregon in the regular season the last two seasons.
Instead of starting out in the top five in the preseason polls, now Oregon opens in the top 10. It's not exactly a slap in the face, but that seed of doubt will be motivating the team all throughout preseason workouts, spring practice, summer throwing sessions, fall camp, and into the season.
There is still the matter of the NCAA investigation into recruiting practices and Helfrich's ability to shape the program and offense over the long term. For now, Oregon still has the qualities to make a legitimate push for the 100th Rose Bowl or 2014 BCS championship game.
Kelly's time at Oregon was defined by speed, but the future of Oregon seems built in such a way that there won't be a quick collapse.
Dan Greenspan writes about the Pac-12 for Fox Sports Next. Follow him on Twitter @DanGreenspan.