Decide to try growing onion in water and in soil, and do a comparison.
Roots growing.
The one in water grow faster than the one in soil.
Spray some neem oil to see if it can stop the rot.
The rot seems pretty bad and smelly. Decide to break up the bulbs, remove all rotten parts, spray some neem oil and observe.
The bottom of onion planted in soil has rotted with some tiny worms (probably are larva of the flies).
The smell are still very pungent, which is probably not a good thing. Have to throw away a cloves as it gets very soft and the leaves are dying.
Rotted slowly.