The sky has fallen on the Oregon football program, if you look at the accomplishments of the Ducks when Chip Kelly was on the coaching staff.

With Kelly as head coach from 2009 to 2012, the Ducks did not lose to mediocre teams. Upsets did not happen. He went 46-7 and led Oregon to four BCS games. Great teams beat the Ducks in UO’s seven losses.

With Kelly as offensive coordinator in 2007 and 2008, asterisks abound, because the Ducks could have been considered among the country’s best teams both years. In ’07 and with healthy QBs, including Dennis Dixon, the Ducks lost only to No. 6 Cal, 31-24. In 2008, the Ducks lost at unranked Cal, 26-16, in awful weather and field conditions — their last loss to an unheralded team until Saturday, when Arizona dominated the Ducks, beating the seemingly flat Rose

Bowl frontrunners 42-16 at Tucson.

The sky used to be the limit for the Ducks, players would say. Now there are clouds hovering above the program and first-year coach Mark Helfrich.

The team has issues, many of which could be remedied in Friday’s 4 p.m. Civil War game against the struggling Oregon State Beavers at Autzen Stadium.

By Saturday, there could be smiles back on the Ducks’ faces. Or deeper frowns.

Quarterback Marcus Mariota’s knee injury tops the list of issues, but Helfrich continues to point to himself as someone who should take the blame. Commendable stuff, considering he makes nearly $2 million per year.

“How we started (versus Arizona), very sluggish in every phase, that’s 100 percent my fault,” Helfrich said, “and I have to figure out exactly what levers to pull and what buttons to push.

“Oregon State’s not going to feel sorry for us.”

Helfrich scoffed at questions about the direction of his team.

“Everybody makes these broad-based statements, whether it’s the game of the century or these guys have to blow up their program because they lost a game,” he said. “No, we got beat. … Flush it and get ready for Oregon State.”

It would be easy to argue that six or seven Pac-12 teams have played better recently than Oregon (9-2, 6-2), which may have dropped to a middle-of-the-pack conference team. Now the Ducks could be looking at the Alamo Bowl or Holiday Bowl, if they beat OSU — or the Sun or Vegas Bowl with a loss.

What are the issues for the Ducks?

* Oregon used to blow away teams early in games. This year, the trend has been the opposite. Halftime situations in the past six games, in order: Oregon led Washington by 14, Oregon led WSU by 10, Oregon was tied with UCLA, Stanford led Oregon by 17, Oregon led Utah by 10, and Arizona led Oregon by 19.

* Oregon doesn’t talk about injuries, and Mariota has tried to remain mum about his knee. Although the Ducks should be held accountable for their “Next Man Up” philosophy, any loss of Mariota’s mobility and role in the zone-read option should not be overlooked.

The Ducks’ running troubles — 405 yards on 98 carries (4.1 average) in the past three games, with De’Anthony Thomas, Byron Marshall and Thomas Tyner held in check — could be attributed to Mariota’s injury. And now, Marshall (foot) has an injury.

* Mariota played the past 3 1/2 games with a brace on his knee, but there has been no sign of backup QBs Jeff Lockie and Jake Rodrigues getting any prime-time action. That might be an indication of the level of confidence the Duck coaches have in their reserve signal-callers. How would the Ducks fare against Oregon State with Lockie or Rodrigues, if Mariota is sidelined?

* Running troubles also point to an ineffective offensive line. The Ducks controlled games with the rush under Kelly.

* The offense had been averaging astronomical numbers, but it has generated just four touchdowns combined against Stanford and Arizona.

* How much does attitude play in Oregon’s struggles?

Thomas and Josh Huff sounded off about not being thrilled to go to the Rose Bowl. Thomas, especially, said it was not a big deal and “whatever.” That points to a team spoiled by its success, and unappreciative, although Helfrich said the comments came from ignorance and lack of context and that “it wasn’t a teamwide deal.”

* Thomas’ comments follow some interesting subplots. How about Colt Lyerla leaving the team after falling out of favor with Helfrich, and then being arrested? How about defensive coordinator Nick Aliotti sounding off on various hot topics more than once — such as the officiating and WSU coach Mike Leach? Thomas said the Ducks should score at least 40 points against Stanford.

Now, the losses and struggles. All such things beg one question: Does Helfrich, Kelly’s former right-hand man and the man Oregon officials hired because of his understanding of UO’s offense and he would ensure continuity, have control of the program?

* The defensive line should have been a seasonlong strength, with ample depth. But Stanford and Arizona dominated the Ducks up front.

The linebackers have not necessarily been a strength, either.

Teams have run on the Ducks — Bishop Sankey of Washington (167 yards on 28 carries, two TDs), Tyler Gaffney of Stanford (157 yards on 45 carries, TD) and Ka’Deem Carey of Arizona (206 yards on 48 carries, four TDs).

And, mobile quarterbacks Kevin Hogan of Stanford and B.J. Denker of Arizona made key plays against Oregon.

* The defense was on pace to be the stingiest at UO since 1980. Not now, after Arizona’s 42 points, 29 first downs, 11-of-16 third-down conversions, 6-of-6 red-zone touchdowns against and 482 yards (304 rush, 178 pass).

The Ducks couldn’t have asked for a better situation to get themselves right — Friday’s game is against a Beavers team that just gave up 69 points to Washington, and the game is at Autzen.

“That pride and work and feeling toward each other will help flush this and rally,” Helfrich said.

The Ducks’ resurgence — which provided the impetus for construction of the over-the-top football facility — started with an epically bad performance and approach in the 2006 Las Vegas Bowl.

“Win The Day,” “faceless opponent,” no “outside influences,” every game’s a Super Bowl, carefully crafting image and restricting media — all the buzz words and philosophy worked for six-plus years.

Now what?

“There are times where you have to buckle down,” Mariota said. “It happens. You lose games. But we just have to come back and fight. We have to control what we can control.”

Helfrich and team leadership will be on the spot in the Civil War, as the Ducks prepare for their bowl game and the program moves forward. Could it be the end of an era? Or, just a blip?

Let Thomas speak for the Ducks about the future:

“I’m not really worried about a bowl game right now. We’re just worried about our next opponent. That’s about it. It shouldn’t be tough at all (to stay motivated). We’ve still got one more big game to play. That’s about it.”

This story originally appeared on Oregon Public Broadcasting.