PassportEX

Yesterday while I was reserving my transmission start making small clattering sound then it suddenly turn into a loud clattering sound and the car stalled out. I turn the engine back on and when I tried to shift it into reserve I can't. Can't even shift it into any gear. No matter how hard you try you can't shift it into gear with the engine on. However, with the engine off I can freely shift into all gears including reverse.

Since I can shift into gears with the engine off I decided to put it into gear first and then turn on the engine. When I do this you can hear a small on and off clunking sound. When it clunk you can feel vibration in the clutch pedal as well. When I give it some gas the noise went from clunking sound to clattering sound. Car does move, but once it start making the clattering sound I stop. After I stop the car the clattering sound continue, but fade away soon after. I let the car idle a little bit then it suddenly stalled out and fall out of first gear by itself.

What can it possibly be? Clutch, flywheel, pressure plate, clutch slave cylinder, clutch master, syncro?

Wharbone

I bet it's one of your flywheel bolts.

Only one way to find out for sure...

PassportEX

Is that the all symptom of a loose fly wheel bolt?

Wharbone

Yes the flywheel bolts could cause that. Could be a broken piece of your clutch too. Only way to know is to remove the transmission and look.

Here's someone with the same problem as you.
http://www.honda-tech.com/showthread.php?t=1593652

Civic2Scooby

wharbone beat me too it. You can get a preliminary check by removing the inspection shield on the bottom of the transmission though before pulling completely.