Water entered brain box, the fan turns but engine cannot start

the fan where?, front of RAD, rear of RAD or blower fan in cab.
all fans can be hot wire tested. even bench tested or in situ.
using a 12vdc battery (large)
old post but,
the "so I shut off" words are very confusing.
tell how you shut what off? AC off? blower off cab.
that thud can be the compressor clutch De_energizing,
most(all) AC have brain box. some are part of PCM/ECU
and the brain cuts AC off for many reasons, but here are some
yes seen them all me. the first 1 saves compressor from wrecking.

1: hi/low R134a pressure too high or too low ,easy test voltmeter
2: engine overheated detected. (saving engine from damage)
3: WOT, the brain shuts off the comp. clutch wide open throttle.
4: in the same vein, the brain shuts off clutch if engine load is 100%
it does that in the hope that you passing a logging truck at 80mph , you, live to tell the story then next day, amazing no?
5: and more,
the brain protects ,you,and the compressor and the engine from damage, all 3 for sure and more.

next time tell what FAN means and where , there are 3 or more fans in the car and cab fan name is blower.
under hood more, even 3. there. even staged by the brain.

lol, no it can't. It can cause unusual issues until it dries out if water got inside it, but not mixing fuel and water on purpose.

The other consideration is that the 'brain box', properly can the the ECM (engine control module) is waterproof. I hose my engine bay down twice a year. I keep it very clean. Never had an issue.

water shorts out the electronics and generally destroys the ECM
replace it with a new or known good unit

Funny usually it wont come on.
I should ask a question first is it on when the car is cold? just turn the key to on before you start the engine when it is cold and lift the hood to check.

If not then there could be lots of things. Engine always hot, worn water pump or thermostat not working properly, bad control relay.

You can check the control relay which is usually mounted on the lower rad support in between the grill and the rad. You should be able to see the relay it has fins on it.

get the correct brain box it is specific to your particular vehicle no other brain box will work.

did the check engine light tell you there was a pcm fault or something else before you did the swap? Alot of things can cause a no start. A bad crank position sensor(CKP) cam position sensor(CMP) fuel pump. My brother-in-law did that to a dynasty and turned out to be a broken wire on the CKP circuit.

brain box it a broad statement no current to plugs could be one of two or three different problems giving the same result

Sorry to say but you need another ECM due to water damage. Seal the next one up with sylicone to keep the water out and don't open it!!! There's nothing that YOU can fix inside of it,and that will just VOID the WARRANTY!

It seems that if you tried that many brain boxes, one of them would have worked.

Here are some things to check. (I am assuming you have gas in the tank, the battery is good and the engine cranks over but doesn't catch and run.) Perhaps one of these items was overlooked in the trouble-shooting:
Engine cranks but won't start:
Charcoal canister full of fuel, faulty MAP or MAF sensor, faulty engine coolant temp sensor, faulty EVAP canister vent valve, EGR valve stuck open, lack of or incorrect fuel pressure (fuel filter, fuel pump, fuel pump relay), water in fuel, fouled spark plugs, faulty ignition module, severe vacuum leak, severely clogged fuel injectors, wrong size o-rings on fuel injectors (prevents compression), faulty airflow sensor (if equipped), Idle Air Control (IAC) valve defective, disconnected-broken-loose wires for all of the above.

The tempreture is above the normal temperature required by the engine there by the coolant sensor will comunivate to the brain box when it is too hot to stop the engine, allow it to cool completely,then bleed the water for the excess air to leave the block engine and the radiator, then try starting,if it does not affect the top cylinder gasket it will return to normal, but also chek for leakage very well.