Gen 2 Prius: Water in trunk -> U0293 code. Radiator fans run at max speed, ICE starts for 15s

Test 12V battery . Check the white plug above 12v battery look at it carefully . All that flooding renders a battery showing volts with nothing behind the volts switch in a load . Boom nothing .

 

Not related to your problem: The water damage you described in Gen2 is common and is likely coming from roof seams you can see under the black roof trip strips as well as areas you can see when rear hatch is up. Clean them and add some silicone or equivalent in the cracks.

What the problem is: The engine is failing to start. The 15 seconds is just the electric motor spinning the engine trying to start it. Keep in mind if you spin an engine that won't start too many times you drain your hybrid battery down and recharging it without a functional engine is a whole other hassle we can walk you through.

Solution: If I were you I'd swap out the ECM after you thoroughly inspected and haven't found any damaged wires. Then I'd probably look at engine temperature sensors to confirm they're working normally. And If that doesn't work I'd look at the spark plugs for clues, maybe use a borescope to see what's going on inside there. Clean and inspect Mass Air Flow sensor and throttle body and all this is assuming you followed @Tombukt2 advice on 12v.

 

Why was the trunk flooded? Did it rain heavily or was the car at least partially submerged? In the former case it is probably the usual sorts of leaks into the trunk and the front of the car would not be affected. However, if the car was actually flooded then all the wiring below the water line is now suspect, including and especially the wiring to the fuel pump in the gas tank. ICE motors don't run without fuel!

Assuming no flooding, parking it in direct sunlight with the doors open (and 12V battery ground lead detached) for a few days might be worth a try. This could still be just "wet wires", and that would help the water evaporate.

Was the hybrid pack actually wet inside? Typically trunk flooding fills up the low points, like around the 12V, but doesn't rise up into the pack.

 

Up here in the Pacific Northwest I'd say 70% of all Gen2 Prius I've worked on have standing water in the rear of the vehicle... It's amazing how many bad hybrid battery packs I've pulled in winter that are wet too. As in we have highest year round humidity in the US up here and we only get a couple-few months of a dry season.

 

Seems like somebody up there in the pack Northwest needs to be pushing these rubber plugs out the back of these Wells in corners of these cars.

 

Yep... It's easier than fixing leaks. Worst case scenario was a 2001 Honda Insight I installed Muddler's Lithium kit in and vehicle's owner had 2-3 gallons in the spare tire wheel well and when she slammed on the brakes hard all the water went forward soaking the circuit board and causing delamination to the traces on the bottom of the board that held water and didn't dry out. Had to replace the whole board after that, which was not cheap.