I'm just reading through parts of the comic again and I realized that I still have no idea what's going on or how papyrus understands it-
Okay! It all begins with Papyrus’ vast interest in knowledge! (Actually he’s just bored, so he wants to read Sans’ science books) Papyrus doesn’t think like regular people, he’s not generally focused on himself but more-so on how he can improve the bigger picture.
He generally has a very curious nature and his only downfall is not fully understanding the concept of normal things/activites. Such as dating, costumes, and work. (His first job was given to him because he did something great, so obviously he believes he just has to duplicate that to become one of the Royal Guard now)
So! Back to what happened with Chara, Papyrus understands the science of it- but the general workings of what he tried to do (create save points) didn’t seem to work for unknown reasons (because Chara needed to die “permanently” for the save points to be solidified in a point of time)
When they extracted power from Chara, it was intended to be concentrated into a secondary machine to help create the save points, however, because of the many resets, and the concentrated power inside the lab. Said power basically collapsed in on itself and made a black hole that swallowed up everything (yes everything)
Papyrus being at the center of that explosion(implosion?) became the most aware of it, even to the point of experiencing a timeline a second time. Like a huge wave of déjà vu he already knew what to expect for a long period of time.
He helped the souls stuck in the “void” to reach out to Chara, which caused a sort of reset. To a point just prior to the event. It allowed Papyrus to prepare and arrange for Chara to reset the timeline once again to “fix” everything. Before they all got swallowed up again.
Unfortunately the ones that were sucked in the first time were still damaged, hence the grey Gaster Followers(And one Goner Kid). Papyrus tried to correct them but their pieces were missing. He managed to protect his brother from a majority of damage and filled as many pieces as he could (Sans is not aware he’s missing pieces, not of his soul, just of his being, that’s the creature that showed up in Sans’ room he created in Snowdin, that thing is what is left of “Aster”)
So now this event caused Gaster to be so readily erased from the timeline that Papyrus had to arrange for both of them to leave and take on new identities otherwise they would both cease to exist entirely, just like the Gaster Followers. Papyrus already saw in the void that Chara’s power was changing, and planned their leave around that.
Before he leaves, he tries to fix any of the gaps/souls that he can, he’s carrying many of the pieces but for some reason can’t locate the missing majority. Which is where he meets… Mystery Man! Quietly sitting in the void. Waiting…
Mystery Man is an amalgamation of all the pieces monsters Papyrus lost in the first event. It’s also got a lot of parts of Papyrus, including his ability to use Wingdings, and a portion of his scientific knowledge.
The biggest thing about all of this, is that it actually would have solved itself rather nicely if Papyrus had accepted his fate and been deleted. :) But in doing so would have doomed us all wouldn’t it?
“I’ll just explain it real quick! It’ll only be a few sentences!” -Me an hour ago