As one of the the fandom's most popular "specific change in the timeline" AUs, I've seen many incarnations of the Genocide Papyrus concept, in which Papyrus takes his brother's place as the Genocide route's final boss. It's both a tragic and compelling concept, as such a scenario would finally give us the chance to see Papyrus' combat abilities without any kid gloves on, as well as providing a veritable goldmine for character development. However, while I have issues with some of the more, let's just say, extreme departures from Papyrus' canonical characterization I sometimes see in these stories, the most consistent problem I've seen is by far the most obvious one: nobody has any idea how to kill Sans.

In order for the AU to work, Sans needs to be killed by the player at some point prior to entering the Judgement Hall, ideally around the time where Papyrus would normally be battled as Snowdin's boss. The problems that arise from this don't need to be elaborated on (frankly, if you know anything about Undertale you already know at least some of them), so in most Genocide Papyrus interpretations I've seen, his death is either explained very vaguely or just altogether ignored. It's an understandable move to make, to be perfectly honest; what gets the plot going is nowhere near as important as what happens afterward, but even so, it got me thinking: while still adhering to the game's rules, tone, and gameplay mechanics, could there be a plausible way for the player to kill Sans that early in the game?

After a lot of thinking, I believe I was able to come up with one, and the best way I can think to explain it is through a step-by-step "walkthrough" of events as I imagine they would happen. So, without any further ados or delays, here is how I would implement a Genocide Papyrus plotline if I had the ability to modify Undertale's story:

The Seven-Step Process

Step 1: Begin a route in which you kill every monster in a given area before killing the area's boss.

I understand there's some fan debate over the name of this path, but for consistency's sake, I will refer to it from now on by its most popular name: the Genocide route.

Step 2: Reach the Judgement Hall.

Step 3: Initiate a battle with Sans at least once.

You do not need to do anything in particular when doing so, just start the battle and let it unfold as it does. You do not need to win - in fact, winning would go against the idea of the alternate battle entirely - but if you do not let the battle begin at least once, you will not get the opportunity to fight Papyrus in his place.

Step 4: Reset your SAVE file.

This is obviously counterintuitive, as it undoes all the hard work you did in order to get that far, but in order to access the Genocide Papyrus battle, it must be done.

Step 5: Begin a second Genocide route.

Step 6: Complete the Ruins as normal.

The events taking place will remain the same as in any other playthrough. If at any time you abort the route by sparing Toriel or by not killing enough monsters before killing her, you will lose the opportunity and the game will continue normally.

Step 7: After leaving the Ruins, successfully kill Sans.

As you might have guessed, this is where the first and most significant change would take place. When Sans approaches you and request a handshake from you, your character will not turn around and accept it automatically. Instead, a text box will appear:

He hasn't caught on yet. Save yourself some time?

Yes     No

This is why Step 3 was so important; through the combined power of Determination and meta-storytelling, you and your character now both know that Sans is going to be the last thing standing between you and the ending you both so desperately want, and he's not interested in going down without a fight. By resetting, you were essentially saying "forget this - I'm going back to the beginning and killing you before you know how dangerous I am".  Admittedly, the player would almost certainly require prior knowledge in order to think to do this, and it does cut a little into the "Undertale should be in a spoiler-free vacuum to be properly experienced" thing Toby was going for... Perhaps in this version of Undertale, where a Genocide Papyrus battle is possible, this alternate path could be very subtly foreshadowed somewhere, turning the most daring and observant of Genocide players toward it.

If you select "No", your first encounter with Sans will continue as normal. But if you select "Yes", you will enter a FIGHT. Sans' will display no idle animation, hand still outstretched from his request, and you will immediately receive the following battle text:

You have one chance.

And then, after giving just barely enough time to process what has happened, the FIGHT button will be selected automatically. Your attack must be precise in order to land successfully; if you press the button too late, too early, or not at all in the time allotted, Sans will jump out of the way, deduce everything you've done up to this point in a matter of milliseconds, and immediately kill you with an unavoidable attack.

And here's the important thing: That battle text you received must be read absolutely literally. If you fail to kill him on your very first attempt, you will not get another chance. If you come back after getting killed, the look on your face will betray you and Sans will figure out what's going on the second the encounter starts. If you Reset the game entirely, playing Genocide through the Ruins for a third time in an attempt to get another crack at killing him, you won't even get the option to make a selection; the text box will appear, slowly display an ellipsis, and then tell you the following:

I   w o u l d n ' t   d o   t h a  t   i f   I   w e r e   y o u.

The only possible way to repeat this encounter and get another chance to access the Genocide Papyrus route is by performing a True Reset.

Is that unfair? No, I don't think so. You're avoiding the Sans fight by doing this, and gaining access to the game's most elaborate and elusive secret. I think it's just as fair as it should be.

The Aftermath, Should You Proceed

In his dying moments, Sans will look at you and figure out everything: what you tried to do in the previous timeline, the fact that he almost managed to put an end to it, and the fact that you fully plan on continuing now that you've taken care of the one thing that had any chance of stopping you. I don't trust myself to write exactly what he'd say in response to this, but then again... what could he say, really? He doesn't have much time anyway - his brother is right around the corner, just a little ways past the conveniently-shaped lamp, and there's no way he could let him see something like this. Sticking you with whatever parting words he can think of, he goes through the familiar animation of laboriously dragging himself out of the battle screen and disappearing... followed shortly by an irritated Papyrus, wondering aloud why his lazy brother isn't at his post.

Papyrus will continue to be distracted by his brother's absence for the rest of Snowdin, growing more and more frustrated with each puzzle he fails to attend. The scenes pass similarly to how they would in a normal Genocide route, with you disregarding Papyrus' puzzles and the town being evacuated and barren, but in the end, Papyrus will not be there to battle you. He's officially up to here with his brothers' apparent boondoggling and, while he makes a valiant effort to leave you a convincing note, he simply can't be put off searching for him any longer in good consciousness; he's got to keep him on the straight and narrow, after all. While not explicitly stated, the implication is that him being mentally preoccupied by Sans is the reason he doesn't catch on to your homicidal behavior the way he would in a Genocide route.

Starting with Waterfall, the route will more or less become what is typically expected of it, with one notable difference: just like any other route where he's alive, Papyrus will start pestering you with phone calls. He will keep you updated on the progress of his searching, informing you that he's tried to contact other monsters to help but they're all "really busy for some reason", and his tone will gradually go from irritated to outright angry as Sans continues to elude him. If it wasn't obvious before, it's clear by then that he doesn't have any awareness whatsoever of exactly who you are or what you're actually doing. The way he speaks gives the impression that he sees all of this as nothing more sinister than a terrible inconvenience to the both of you; he had to postpone your battle and inevitable capture in order to do this, with his updates being frantic and awkward attempts to save face.

One additional note about Waterfall: the scene in which Papyrus talks to Undyne within earshot of you is included as in other routes where Papyrus is alive, but it's clear from Papyrus' reactions that her attitude is very different than it is in those routes. Plain and simple, she has no idea what to say to him.

Come Hotland, and Papyrus' calls go from angry to worried to outright terrified. Everybody in the Underground seems to be gone at this point, including Undyne, whom he trusted to help him more than anybody else, and Sans is still nowhere to be found. He still has yet to catch on to his exact fate, but it's obvious that thoughts of something very bad happening have finally started to break past his walls of naivete and innocence, however he fights to deny them and stay positive. In sheer desperation he'll eventually ask you, the only person who isn't either dead or hiding somewhere without any cell reception, if you have any idea where his dear brother is, and there will be no option to answer.

Just before you enter the Core you will receive your final phone call from Papyrus, the shortest one of them all, and it will notably be the first time in the game he speaks without capitalizing every letter:

"Human..."

Eventually you'll make it to the Judgement Hall. The cutscene in which you are forced to stop as the camera pans over to reveal Sans will play as it always does... except, of course, there will be no one standing there. The hall is empty. How satisfying. You'll then be free to move once again and you'll press on forward, all the way to the end of the hall, when... right before your eyes, the exit is suddenly blocked.

Blocked by an arrangement of bones.

Additional Notes

• The reason I structured the plot the way that I did is because, realistically, I think the only thing that could drive Papyrus into no-holds-barred killing mode is a state of blind fraternal outrage. The shock of losing Sans would need to happen very shortly before the Judgement Hall, otherwise he'd have enough time for everything to sink in and couldn't bring himself to do it.
• I didn't elaborate on the actual battle because I wanted to write a plausible set-up for a Genocide Papyrus battle, not a Genocide Papyrus battle itself. That, and I still haven't personally decided which interpretation of Genocide Papyrus I like best. As far as I can tell, pretty much any version you prefer would probably fit just fine, unless of course your interpretation actually requires Papyrus having time to let everything sink in.
• While many would consider it a wasted opportunity, it would of course possible to abort a Genocide route after killing Sans. The impact of his death would, of course, be a significant one: many NPCs will express irritation at Papyrus' constant nagging to help look for him, believing he "probably passed out in the forest somewhere again and will turn up again in a few hours with a killer of a hangover", while others who are closer to the brothers will express more sympathetic concerns. Most notably, Undyne's pre-battle speech will have a similar deadly tone to the one she delivers if you kill Papyrus, not because she was particularly close to Sans but because she knows full well that she can't hide his death from Papyrus forever. The Judgement Hall will be completely empty, and if anyone wants to speculate how the new branch of possible neutral ending phone calls might pan out depending on who else you killed, by my guest.