2006 Civic ex had dead battery, just over 2 volts dead. It managed to take a charge after several hours. Tried to key start and get the green transponder key light flashing on dash. Turns over, won't fire. Most of what I've read says it likely needs keys reprogrammed.
Had a locksmith come to reprogram. He gets an error every time he tried, says maybe something wrong with the ecu. However years ago I installed a r/s with transponder bypass and it will still start the car. Remote start, then key in, turn to ON as you normally would, and it will drive away. If I key to ON first then try to r/s it already doesn't like the key and it will turn over and not start, just like if I try a normal key start(green key light flashing). The transponder bypass does not house a spare key, rather it learns from a key in ignition(communicates through single pink data wire) so it shouldn't be 'stuck on' and interfering. But just to test I've unplugged it and tried the key with no luck. This unit was also unplugged while the locksmith was doing his thing.
Is it possible the transponder reader ring died? I even removed it, let it hang(still plugged in) and keyed ON and got green light flash which is what it should do without seeing a correct key anyway. Same thing if I stick one of the keys in the ring and use the other in ignition.
Also to note, battery was replaced prior to locksmith showing up.
I appreciate any help. This car has been a champ, about to roll 240,000 miles and has needed the least parts replacement of any car/truck I've ever known. I feel like if it goes to the stealer it's gonna cost a bunch of money for them to say they can't figure it out, just a hunch.
Thank you

 

borrow obd2 code reader and see if you can read anything off of the ecu. locate main fusebox and check the ecu fuse isn't blown.

 

^^^^^^^^^This guys right.....sort of.

A code reader likely wont pull immobilizer codes, you probably need a full functioning scan tool for the codes. Until you do scan for goods, this is a guessing game and your guess is as good as ours......

 

I metered all the under dash and engine compartment fuses, none were blown.
I was turned onto a tsb on a different forum that seems to fit the situation exactly.
https://f01.justanswer.com/pyZ...161549_civic_jump_start_06.pdf

Honda tsb 06-036

I then started to search for info on the MICU and immediately found a thread that talks about door activated map lights staying on all the time, and it being an issue with the MICU. The night after the locksmith tried reprogramming keys I walked by my front door and noticed the lights were on in the civic, was this exact issue.
So that, plus the tsb pointing to the MICU for my no start issue tells me that's the direction I need to head.

 

Check to see if you can get one from an Acura TL/CL. It may not be relevant but I had to replace the transponder key ring for my old '00 Integra. The replacement was from a '04 CL.

 

its just to see if the ecu functions

 

The ecu is fine. As I had stated I can still remote start it and drive. Furthermore I was driving it yesterday and my persistent p0497 came back which I was able to erase. I also obtained the immobilizer brake code for it the other day and that works as well.
I'm waiting for an micu to arrive, will replace and bring the car to a dealership to register it to the car.

 

To update, because it's frustrating when people don't lol

I ended up replacing the driver's side MICU with a used one. Brought it to a dealership and they reprogrammed/registered it to the car as the tsb states.
All is well now, starts with a key like a normal vehicle... Paid $84 shipped for the used unit, 1 hour labor @$115 for the 5 minute program procedure.