you haven't said what make and model scooter you are referring to and what kind of ignition system you have fitted so we are rather limited .
Have you tried pulling the green alternator wire out of the junction box and checking if you get a spark from the green alternator ignition wire to chassis earth when you kick the engine over ?
if you get a spark then the alternator ignition coil is probably ok. Next trace the Green wire from the junction box to the coil or CDI box or rectifier (depending on which model you have)

and make sure the green wire is not cut or trapped or shorting anywhere. Check your connections are clean
Remove and clean your earth strap
After that its difficult to help further without knowing more about your scooters specs