How a Manual Transmission Works

A manual or standard transmission is the alternative to an automatic transmission, controlled by the vehicle's driver with the use of a gear selector and a clutch pedal assembly. The manual transmission has less moving parts and is more fuel efficient, stronger and less expensive to produce than its counterpart. The gear selector or shifter is located at the center of the passenger compartment between the driver and passenger seats and will display the shift pattern of each gear including reverse, first gear being the lowest and fifth or sixth gear being the highest selection.
gear selector

Because the manual transmission is a direct drive to the differential and drive wheels there must be a controllable coupler between the transmission and the engine that can be disengaged when the vehicle is at a stop, and then engaged when the vehicle is in motion. This device is called a clutch which is positioned between the transmission and engine and is activated by the driver using the clutch pedal, pushed down to disengage, while allowing the pedal to rest in the upward position leaves the clutch and transmission engaged.
clutch pedal

Here is what the manual transmission looks like still attached (bolted) to the engine with the transmission cross member removed for easy viewing, at the rear you can see where the driveshaft is attached which bolted to the differential.
standard transmission

Inside the transmission is a series of gears, bearings, shafts and Synchros which are used at various times during the transmission's operation. These components are lubricated by transmission fluid or gear oil inside the case. Most transmissions contain three shafts: input, output and counter or lay shaft in which the gears and bearings reside. Syncros are designed to slow gears to a stop before they are engaged to avoid gear grinding, when these Syncros wear out the gear remains spinning which produces a grinding sound. Gear quantity and ratios are designed into a particular transmission to perform a specific task by the manufacturer. In the image below you can see the gears and bearing but the Synchros are hidden inside the body or each gear and are un-viewable.
standard transmission cutaway

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