If the battery is completely discharged, even the kicker won't start it. Agility 50 has a dc cdi and needs some power in the battery to make a spark. If the battery is too low to crank it but still has a little power left you can start it on the kicker, but not if it's completely flatlined.
If water got into your electrics your battery is probably completely flat, and you may still have a short in there. It's possible that draining through a short could have damaged your battery too.
1: charge the battery and take it to a battery shop and get it load tested. If it fails the load test, replace it. If having a known good battery doesn't solve your problem, don't leave it connected between troubleshooting sessions because you don't want it to discharge through a short again.
2: go hunting for shorts with a multimeter. Fix any that you find. Check for loose connectors while you're at it.
3: with the plug removed and grounded against the block, crank it and check for spark. If not, go back to #2 and check again for any shorts or loose connectors you might have missed. Go through the wiring harness with your meter looking for bad runs that may have a break you can't see as well.
4: Good battery, no wiring faults, good plug and still no spark? Now you're looking at replacing stuff. Coil & plug lead or cdi is probably toasted.
If you get all the way down here and still have no spark, I'm out of ideas. If you do have spark and it's still not starting, you're looking at a fuel or air issue.