The 1999-2000 Honda Civic Si commonly has mechanical issues with the manual transaxle.
Drivers will notice that upon decelerating, the transmission will shift to neutral on its own, and some gears, normally second, will be difficult or impossible to select with the gear selector. Lastly, a grinding noise accompanies these issues. It changes with engine speed, and comes from the transmission.
The engine connects to the transmission with a clutch and shaft. The clutch engages or disengages the transmission input shaft, and the transmission input shaft drives the transmission. The input shaft is held in place by bearings which allow it to spin. When those bearings fail, the input shaft can move, and the problems noted above become very evident due to the loss of synchronization of the transmission.
To correct the situation, the transmission must be removed from the vehicle, disassembled, rebuilt, and reinstalled in the vehicle.
The best way to ensure this doesn’t happen to you is proper maintenance of the transmission.