2016 Lexus GX460, 105k miles, just bought used here in Portland OR, religiously serviced at the San Antonio Lexus dealer (carfax records).  OEM Battery 4 yrs old in 12/24.  Hasn't passed Oregon emissions testing 3 times...everytime same (4) emission monitors at "unready".  Fuel between 1/4 and 3/4.  Did a Toyota "drive cycle" procedure and a generic high speed cycle over 150 miles.  As I was about to return the vehicle to non Toyota dealer who sold me a car that can't pass emissions (2 Oregon laws broken, 1 federal) the car would only stay running 1-3 seconds then die.  Swapped fuel pump relays.  Checked battery with tester:  still labeled "good" but voltage 'medium' at like 11.7v.  I charged the battery with smart charger...initially showed 60% and waited until 100% charged.  Car still wouldn't run.  Towed it to nearby Toyota dealer who initially had to do a hard handshake with one of the computers (start signal sent but not returned).  That got vehicle running for dealer to perform another drive cycle to no avail.  They suspected the "immobilizer"  However, couple days later they say battery isn't holding charge.  I replace the battery.  Now for the last 5 days they cannot replicate the non-stay running problem after many tries daily. They have an open case with Toyota engineering who wants dealer tech (lead tech at that assigned to my case) to capture a "waveform" when the problem occurs.  At this point, if problem not recreated by this coming Tuesday, I will pickup car and take to purchasing dealer to resolve the emission failure condition.  Toyota dealer also checked for moisture in PCM (maybe ECU), checked fuelpump module, fuelpump and ensured there were zero software updates available for the vehicle. Nor were there ANY matching hits within the service bulletin database. There has NEVER been any codes via ODB scans nor has there EVER been CEL or other lights on the dashboard. 

Occum's razor principle says the simplest explanation is likely the likeliest one (bad battery) and I read, with lots of Artificial Intelligence searches, that random/bad voltages from the battery can cause both problems I'm experiencing.  I read the ECU stores the actual emission data while things like the PCM (powertrain control module) collects emission data from things like the O2 sensor.  So unless the ECU and/or PCM are bad...the problem(s) may have been resolved by a simple battery swap.  But WHY!@!@  Isn't the battery in conjunction with the alternator supposed to act like a voltage regulator and provide a steady state level of voltage (unless the alternator bad...on a Lexus after 105k miles?). 

It seems the non stay running problem resolved but it could be a ticking time bomb waiting to go off.  I won't know if the new battery ALSO has resolved (I read poor voltage can prevent the ECU from storing values and/or corrupting the KAM (keep alive memory) the emission monitors until there are adequate drive cycles AND confirmation via ODB2 scanner.  I know IF the ODB2 scanner shows those monitors as "ready" the car will pass emissions.

The lead tech is at a loss, I'm at a loss and as a very curious person, REALLY would like a very educated guess as to likely culprits along with a better understanding of how this can happen.  

FYI - I and the tech checked and zero evidence the vehicle was ever submerged. Again, I can see how well the vehicle was maintained at the Lexus dealership.

Stan