It happened around 12:20 a.m. near Ocean and Flatbush avenues in the Prospect Lefferts Gardens section.
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Authorities say the bus operator was driving a Q train shuttle bus, which only picks up passengers at Q stations where there was no subway service due to overnight repairs.
The 39-year-old driver was between stops when one of the suspects asked to be allowed to board, officials said.
He advised the man that he could board at the next bus stop.
As the bus was paused at the intersection, authorities said the man forced open the rear door, threatened, spit at, and attacked the driver.
"He wanted to get on between stops, and the guy was irate and obviously extremely angry," TWU Local 100 Vice President J.P. Patafio said. "Ripped open the back door, and that's when everything started."
The driver was stabbed in the stomach and slashed him in the face, cutting him over the eye, according to officials.
Police also say that while the attack was taking place, two additional men boarded the bus and threatened the victim with a boxcutter.
Those two suspects fled southbound on Ocean Avenue while the other attacker, a man in his 30s, fled eastbound on Empire Boulevard.
Police released surveillance images of the three men they are looking for.
The victim was taken to NewYork-Presbyterian Brooklyn Methodist Hospital in stable condition.
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He's expected to survive.
"We are working closely with investigators who are determining the facts of this incident," MTA Chief Safety and Security Officer Pat Warren said. "Violence against transit employees or riders is never acceptable, which is why we worked so hard in Albany to pass a new assault protection bill."
It's the latest in a series of attacks on transit workers, and just three weeks ago, workers rallied to demand police patrols and compartments -- rather than partitions -- to protect drivers.
The driver in this case got up out of his seat, but union officials insist he had little choice once the rear doors were broken.
"When the bus is taken out of service, and the back door is broken, the operator has to make sure everyone gets off the bus," Patafio said. "He has to inspect it, and he has to make sure everything is orderly. And I think when he gets out of that seat, that's what he's trying to do."
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Unless more is done to protect drivers, union leaders put the MTA and its riders on notice.
"What I'm saying is if we don't feel like we're getting the respect and the safety that we need, the city could shut down," Patafio said. "I'm telling you this, my members are going to act. They're gonna act. And they're going to act because they're frustrated. Buses aren't going to roll down the streets as if nothing is happening while operators are getting stabbed, spat at, cursed at and disrespected."
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