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I put my 2005 Monster 620 away last winter and everything was working normally. The battery was disconnected when I put it away. I pulled the bike out a few months ago to charge the battery and let it run for a bit. No problems. Well, I forgot to disconnect the battery after that and when I pulled the bike out a few weeks ago I noticed there were mice living in the airbox, and the 40A main fuse was blown. The fuse could have blown from the mice or from me washing the bike, I'm not sure I didn't notice until after a wash. I replaced the fuse and started it up. The normal startup procedure happens, the pump primes and the cluster does its sweep. The immobilizer light flashes at me twice then stays on and the starter switch does absolutely nothing.

TLDR; The immobilizer light flashes twice and the bike refuses to start. I've replaced the antenna, replaced the battery, tried two keys, tested all the fuses and relays, and inspected the wiring. Everything looks fine and it still won't start. Does anyone have any other ideas or tips? I'm at a loss here and I really don't want to buy a new ECU.
 

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I don’t know what the attraction is but mice (and rats) like to chew wiring. It won’t cost to anything but time which would be well invested visually checking all your wiring loom for signs of rodent damage. Like you said in your earlier post, it ran before you put it away.
 

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Similar happened to me. Go over the wiring, pushing wires back into their connectors from both sides. Some of mine had partially unplugged themselves internally over the winter.
Why ? The zip ties from the factory were installed too close to connectors. Move them further away. I also carefully cleaned all the connections to the ECU, and ran a ground wire
from the spot the factory grounded the ECU over to the main battery ground point on the frame. The factory ECU ground on my bike was attached to plastic !
 
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