In the alternate timeline, Helen, Sam and Karen are on community service as a way of keeping their superhero identities a secret. Whilst walking around the estate, Neil throws a can on the ground and is asked to pick it up by Helen, to which he responds that it is what they are supposed to be doing. Angered by this, Sam uses his power of Flight to take Neil up in the air and drop him from a great height. He is killed on impact.
The alternate timeline is later erased, thus Neil's death never happened and he is still alive in the current timeline.