I have a 1999 gs300 with starting issue. On occasion ( more often than not as of late) the car will not start and only crank. When I put the key in the ignition the security light will not turn off like it is supposed to. The lock actuators for both front doors do not work ( has been this way since I purchased the car 2 years ago) so they need to be manually locked and unlocked. It seems that this might have something to do with the issue but I cannot say forsure. When this issue occurs what seems to work best is playing with the lock/unlock both with the fob and manually. Then when I let the key sit in the on position in the ignition for awhile is will usually start ( with security light still flashing). Once it has been started and ran for a bit, I am able to turn the car off and take out the key and if I re-insert the key the security light will go off and the car will start up right away with no issue. Worth mentioning: my key is the original key and is very old, has a crack in the housing of the key as well. What might be causing this issue? It happens enough to make me not want to drive the car anymore for fear of being stranded somewhere.

 

Have you replaced the fob battery yet? It's a CR1616

 

Yes the remote battery is new. The remote has no issue *attempting* to unlock the car doors as when I hit the lock and unlock buttons they work fine for the rear doors just not the front doors

 

I also had intermittent not-starting issues. Crank, but no fire. My issue was the engine immobilizer. I went like this:
I put the key in, but the immobilizer light keeps flashing, causing the engine to crank but not fire. This happened on short stops, like getting gas. I found I had to exit the car, lock the doors with the key fob, and wait a few minutes. Then I unlocked the doors with the key fob, get in, insert the key into the ignition, and the immobilizer light would turn off, and now the engine cranks and starts.
I also found I could turn off the immobilizer (to allow the car to start) by disconnecting the positive lead from the car battery for a few seconds. Then reconnect it, tighten the nut, close hood, get in car, insert the key into the ignition, and the immobilizer light turns off; engine starts.
I finally found the cause: One of the connectors under the steering wheel column was not making good contact. I dug down into them one day, grabbed each end of the fasteners, and jiggled them in/out. Now the immobilizer problem is gone.

 

Did your car also not have cel, no battery light with the no crank and security light?

 

mine does please tell me you figured it out. Im desperate

 

Multiple problems seem to associated with the Body Control Module, BCM, which controls signals from the dash, ignition key, door locks, lights, wiper, horn ect.

Easiest is to buy an used module in the market and swap it in. It's under the dash, only a few connectors and bolts/nuts. If BCM is not the cause, you can always resell it.