Maybe you're thinking about the emergency "brake" cord ? That works the same way in NY subways. They alert the driver and conductor to a possible problem in a train car so that they can get police assistance and/or bring the train to a controlled stop.
The emergency brake that is discussed here is different. It's inside the operator's locked cab, and releases air brakes that stop the train with maximal acceleration to the extent that the wheels can be damaged by grinding against the rails. They are only used in a last resort but they have to be available and functional in the event that the human operator finds itself unable to make a controlled stop. The same subsystem activates when the train incorrectly passes a red signal or hits a large obstruction in the tracks.
TFA explains the break is located an area that should only be accessible to MTA personnel
>He climbs aboard the rear of the train as it departs a station, unlocks the safety chains, somehow gets into the rear cab, and triggers the emergency brakes.
The emergency brake that is discussed here is different. It's inside the operator's locked cab, and releases air brakes that stop the train with maximal acceleration to the extent that the wheels can be damaged by grinding against the rails. They are only used in a last resort but they have to be available and functional in the event that the human operator finds itself unable to make a controlled stop. The same subsystem activates when the train incorrectly passes a red signal or hits a large obstruction in the tracks.