DENVER — Chipotle stores across the country opened several hours late Monday so the company could address food safety issues that have plagued it over the past few months.

A criminal investigation is underway into the fast casual food chain’s outbreak; some believe the outbreak might not be bad food safety practices but an act of biological terrorism.

When an E. coli outbreak hit one of Colorado’s biggest success stories, Chipotle’s stock tumbled as consumers shunned the food chain, frightened about contamination.

But there’s an emerging theory that’s gaining momentum: Chipotle wasn’t to blame and someone targeted the company or its suppliers using bioterrorism.

“It is possible that someone went into Chipotle and sprayed those pathogens so somebody got sick. … In fact it’s the most likely explanation,” said Alan Lewis, a policy expert on natural foods.

Lewis said it may have to do with a recent position Chipotle took against genetically modified organisms and the concern over their link to herbicides.

“Out of the blue, shortly after Chipotle takes a stand on GMO. They suddenly have a food safety problem. … This is what is raising everyone’s eyebrows,” Lewis said.

Herbicides kill weeds but not GMO crops. These foods have been genetically modified to be resistant to the chemicals. It means farmers can save money because they don’t have to hire people to weed their fields.

It also means the fields are soaked with chemical herbicides and no one really knows if that’s dangerous or not. GMOs are a $15 billion industry and reputation matters.

“There are corporations that have bet the farm, pardon the pun, bet the farm on the GMO,” Lewis said.

Health blogger Mike Adams first put forth the theory of bioterrorism and admits its controversial.

“They operate with a criminal mindset, so it is consistent with their behavior that they would attempt corporate sabotage against Chipotle, the leader in clean fast food,” Adams said over Skype.

Chipotle said in a statement it has “seen no evidence to support this.”

But the Centers for Disease Control and Prevention is stumped. In its final report on the outbreak, it said: “The investigation did not identify a specific food or ingredient linked to illness.”

Experts say that’s unusual and telling.

“If Chipotle had an unsatisfactory food safety system, I think they’ve been around for 20 years, you would have seen this throughout their locations,” Lewis said.

A criminal investigation is underway, but when asked whether the focus was internal or external, Chipotle declined to comment.