So many possibilities. Very hard to diagnosis without knowing what the alarm was for. I'm guessing maybe a water temp alarm or exhaust temp. alarm, since they are more common problems on that ski. Have you replaced the cat/con with the D-plate? The cat/con can fail on those skis and cause the ski to shut down and not start. Maybe your son ran over something and clogged the cooling system, which would activate the water temp. alarm? Look in the pump to see if anything is stuck in there.
Next thing to check for is loose electrical connections. Could just be a loose water temp. or exhaust temp. sensor, etc.. I'd look at all connections including in the Ebox first. Loose, bad, or corroded water temp. sensor will prevent spark.
Make sure you have a good battery..........take it to an auto parts store and let them load test it. Could have been low voltage alarm on the battery. You could have enough juice to light the start display, but not enough to crank the engine.
If you have done the above without success then you will either need to get the service manual and follow the troubleshooting guide to test the electrical system, or take it to a dealership to let them do it.
There are many other possibilities, but less likely IMO since they would probably not be associated with an alarm: bad starter solenoid, bad pulser coil, bad stop/stop/kill switch, something locking the pump system, the list goes on and on..........