This happened to me too. I assume you've checked the obvious like replacing the battery in the fob.

My case was a little extreme because I had to replace the alternator on the trail and I disconnected the battery to do it. Of course when I reconnected the battery the car wouldn't start and the fob was at home about 400 miles away. I ended up ripping out the entire alarm system. It was actually easier than I expected. There was only one wire under the dash that needed to be soldered back together before it would start.

'96 SR, 35's, body lift, arb front bumper, Custom rear rock bumper, rock sliders.
'89 Raider V6 w/ SR rear axle & locker
Kirk's Montero page but not updated in forever
KJ6GVJ