Lexus RX400h message 'Check Hybrid System' and it wont start I took out the small battery i charge it I let it for 2 hours but still nothing

Your Lexus's "check hybrid system" warning light means that something is malfunctioning in your vehicle's hybrid system. It could be a problem with the hybrid battery, but it could also be a blown fuse, a faulty fuel pump, or an inverter failure, among other issues. Cold weather can sometimes trip the system, too. your starting battery may be bad

VSC could also be battery problems

Disconnecting the battery will clear any codes in some cases.
Wait until it happens again and scan it then, for clues.

2006 Lexus RX400H hybrid .
and long story.(you added and very very good)
and if was mine, my story would be same, park it and wonder what to next.?
this car is very complex, unlike ICE real cars were simple and still are to a good extent.
I do wish you find a good shop to cure all that.
a full service manual in hand may do the trick.IDK.

good luck! and be SAFE.

use the scan tool as the hybrid starts and fails to light off the engine, see DTC code for that.
scan before ,during and after failures
and use the pending button too on t he scan tool as here may be marginal or intermittent failures

also (Im no hybrid guru) but some hybrids do not run the engine (to save fuel) until the battery has some amount of discharge detected.
some even have switches to set the mode you want,save fuel or save battery life, IDK this car.

If the engine is running more often I would be checking the condition of the batteries. The whole idea is to run on the batteries until the voltage becomes too low in which case the engine starts. Take it back to the dealer service department for a diagnosis of the problem.

Can you ensure the car is in park?
Move lever to D and then back into Park and see what happens.
I have heard with this particular model, we have the environmentally unfriendly RX 330, that the batteries lack of charge may play havock with the electrics in these cars.
I religously charge my battery every six months with a smart charger so its always in peak, I also find a quick zap at the first cold snap of autumn / winter gives us trouble free motoring.

Does it still have a warranty on it? If so I would use that while you got it, and get it fixed free of charge. There is probably a cosmetic plastic cover hiding the alternator. However if you locate the belts than it will lead directly to the alternator.

Trying to get past the right way is a good way to get killed ( don't try to. )

Put a new battery and go through an electrician to see if the alternator is charging the battery

if this car has the daytime running lamp option they are supposed to be on.

Hey Guys, The problem is that the 12V battery is low or dead. Having the battery replaced will fix this issue. (I have the same vehicle, had the same problem, and this was the fix)