Fire set the night sky of Flushing aglow early Wednesday morning when a blaze broke out in two commercial buildings on the north side of Roosevelt Avenue between Main and Union streets.

It all started at 2:15 a.m., when the third floors of 136-13 and 136-15 Roosevelt Ave. went aflame. Firefighters came to find the blaze so intense they couldn’t enter. Instead, they used a tower ladder and two hand lines to tame the fire.

“It’s pretty rare that a fire is so bad we’d have to do that,” said Deputy Chief Charles Clarke of the 14th Division.

Three firefighters suffered minor injuries and are expected to recover quickly.

A day later, the structures were determined to be so unstable the City plucked apart their remains and sent them off on dump trucks.

Several small business owners were able to freeze the demolition after pleading with Fire Marshals and members of the Office of Emergency Management. They spotted a cabinet that housed vital documents, including passports and money, which the large excavator plucked out and placed on the ground.

The cause of the fire was still unknown by press time. The FDNY recovered all materials they would need to conduct an investigation before the buildings were torn down. But given the nature and timing of the blaze and prime value of the property, nefarious causes were not ruled out.

“It’s too soon to tell the cause of this fire or if there was any foul play,” Councilman John Liu (D-Flushing) said. “We’re very happy and fortunate no one is hurt.”

Members of Tower Ladder 160 still loomed over the buildings the morning after the fire, dousing the remaining smoldering husks as onlookers pulled out cell phones and snapped pictures. Most seemed stunned yet mildly entertained by the sight. But mixed into the crowd were workers and managers of the charred buildings, wondering what hit them.

“I don’t really know anything at all,” said one store manager, who demanded to remain anonymous, fearing retribution from the company. “My guys are still going to get their pay though, that’s for sure.”

The City projected the property’s market value at $1.3 million in September, while its assessed value was $604,500 as of July. The two buildings housed a Payless Shoe store, Taco Bell and two beauty salons.

The blaze also caused a commuter nightmare. The No. 7-train suffered a brief lapse in service and buses were rerouted around Roosevelt Avenue at its intersection with Main Street.

The buildings are registered for multi-store commercial use, which would not allow private residences on the property. Firefighters found no one in the buildings or on the streets when they arrived. Still, some officials believed the building’s top floors were illegally occupied.

“You won’t find the business owners here,” said one FDNY official at the scene, who requested anonymity because of a lack of clearance to speak to the press. “They’re busy being grilled over the cause of this.”

On Thursday, Liu, flanked by business owners and representatives from the Flushing Business Improvement District and the City’s Department of Small Business Services, announced a plan to help those affected by the fire.

“They have lost everything they worked so hard for,” Liu said. “With the help of these city agencies, we can get them back on their feet as soon as possible.”