The two times Jonathan used that gun was to save Spidey from a monster and to save 4C from Himself.

Because of 4C's memory loss he likely only really remembered Spidey and Jonathan when they were concerned about him and planning on how they were gonna kill him, but he still felt like something was wrong and kept asking them about it. Even if he didn't remember his soul did.

The first time session ended Spidey was with Jonathan and 4C, the second time she was with only Jonathan, the third she was alone, the fourth she was with all three again because she and Jonathan were watching 4C in the moon.

There is a chance that Spidey will either grow to be kinda like Jonathan if she survives to an older age, or maybe like Chuck. Either cold and a bit of a hardass, or absolutely insane, and as Chuck put it in the start, "There's nothing to smile for, so its best to always smile!" I think she may grow to emulate that saying.

There's also a chance Jonathan will either go hyperprotective of Spidey since they've already lost 4C, or he'll push her away moreso then originally because he can't handle even more loss.

They were doomed the second the three of them became a found family.

They were doomed the second 4C originally got lost.

They were doomed the second they got worried about 4C being lost the second time.

They were doomed the second they both froze upon finding 4C again.

They were doomed the second Jonathan took a moment to warn Spidey and 4C about the monster instead of letting them be bait so he could get away.

They were doomed the second Jonathan and 4C comforted a sobbing Spidey in the warehouse after they were chased.

They were doomed the second Jonathan shot the monster for Spidey then told 4C the bullet had been meant for himself.

They were doomed the second they grouped up.

(Added on bit that has a bit of horrors!!!)

Do you think 4C suffered? A shot to the back of his head and it failed to kill him, while Spidey struggles to reload before throwing the gun at Jonathan saying she CAN'T do it, while 4C is bleeding out, already in pain from the infection, and in more agony from the shot.