Fact it starts at all and runs for 3-sec. shows it’s mechanically sound. Has compression/air, has correct amount of fuel, and has sufficient spark to set off that mixture. All systems are working.
I believe ‘12 and later Ninja 300 have immobiliser system with matched key and ECU. When starting, ECU checks for matching ID on chip of key. If it doesn’t match, ECU cuts power to fuel pump. There may be enough fuel left in system from initial priming to run for 3-sec and that’s it.
Usually when ignition-switch needs to be replaced, it’s configured by locksmith or dealer to use original key to maintain matching ID with ECU.
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