18-year-old Bates -- one of the top prospects in the class of 2021 -- was pulled over in Superior Township, Michigan after allegedly running through a stop sign around 10:45 PM on September 18.

During the traffic stop, Washtenaw County sheriff's deputies -- who immediately recognized Bates -- told him there was a strong scent of weed coming from his vehicle and asked if there were guns or drugs in the Mitsubishi Outlander.

Bates -- who was driving without a license -- initially claimed he didn't, but eventually came clean ... admitting he had marijuana and a gun, putting his hands up and complying with the officers.

The 6'9", 190-pounder was then placed under arrest and put into the back seat of the cop car. While his vehicle was being searched, cops allowed him to use his phone ... and he called his mother to apologize for the arrest -- breaking down in tears in the process.

During the search, cops found what appeared to be a bag of marijuana ... as well as the gun.

Emoni's mom, Edith, calmed him down during the phone convo ... and then handed the phone over to a man, who seemingly said he is the owner of the gun.

The man appears to ask if cops found "my stick in your car?" ... to which Bates replied, "Yeah."

Bates was hit with two felonies -- carrying a concealed weapon and altering ID marks on a firearm -- but on Thursday, Bates' attorney, Steve Haney, told ESPN he expects the charges to be dismissed after agreeing to a plea deal.

Haney says he will plead to a misdemeanor count of attempted illegal transportation of a weapon ... which will be dismissed off his record if he completes a diversion program.

The school confirmed the news to TMZ Sports ... saying, "The Eastern Michigan University department of athletics has received notification that there is an agreement between the Washtenaw County prosecutor's office and Emoni Bates' defense team that would result in the felony charges being dismissed."