"heh, sorry kiddo. it appears there's been a bit of a... mix-up."
– Sans after he realizes what's going on.
When he confronts Chara in the Judgement Corridor for their fight, Chara suddenly disappears and in their place is a very confused Frisk. Thinking they are still Chara, Sans attacks them with a Gaster Blaster until they are lowered to 1 HP and becomes shocked when "Chara" begins calling out to the people "they" murdered.
After a few moments of his own confusion, Sans realizes there has been a mix-up in the timelines. Once he is sure that the Frisk he is facing isn't Chara, Sans takes them to Grillby's, abandoned after Chara's rampage. There he explains to Frisk that he has had dreams about them (Frisk) where they freed the monsters from the underground and that Chara was not that person. This Frisk is the one that Sans had been dreaming about.
When Frisk begins to understand that they are in Chara's timeline, they realize that Chara is in their timeline. Sans tells Frisk that he know how to get to the other timeline in order to save Frisk's friends. At first, he is reluctant to do it, but he decides that he has to.
Travelling to the Neutral timeline, Sans finds Papyrus mourning the untimely death of that timeline's Sans (indirectly caused by Chara's actions) and hugs him before crying into his shoulder. He then notices that Papyrus is covered in monster dust and he believes that Sans has pulled another prank on him.
Before he can put two and two together he is confronted by Toriel who apologies to him, with Sans only vaguely recognizing her, and by Alphys who seems to know what Sans did in order to crossover to the timeline and reminds him about what happened to 'him' (Gaster) and about their agreement. Sans replies that he does remember, but states that in his timeline, "There was no point..."
Sans looks exactly as he does in Undertale. However, his clothing has a darker shade of colour than his Pacifist counterpart. This is most likely to tell the difference between them and due to the dark atmosphere of the Genocide Route.
Unlike his Pacifist counterpart, Sans from the Genocide Route almost never makes any puns and is generally a serious character. This is first noticed by Frisk when Sans gives them a Hot Cat they mention that his hand didn't even have a whoopee cushion in it. Sans is shown to start brooding whenever Frisk asks where everyone is in Sans' original timeline, showing his remorse for Chara's victims.
Despite the fact that he annoys Papyrus a lot, Sans cares very deeply about his brother. When Chara kills Papyrus Sans is overcome with grief as he could have prevented both his brother's death and the deaths of many of the Underground's residents. When he goes to the Neutral/Pacifist Route he is overjoyed to see his brother again.
Sans and Chara's Relationship is however, They Hate each other. Since Chara killed Papyrus, Sans is slowly Getting Hostile to Chara.
Sans and Alphys made a promise about something related to crossing timelines and W. D. Gaster, which Sans broke to get Frisk back to their timeline.
Since the two never met in the Genocide Route, Sans only vaguely recognizes Toriel when they meet after crossing over to the Neutral/Pacifist timeline.
W. D. Gaster
Gaster seems to have a connection to how Sans and Frisk were able to cross to the Neutral Timeline, which is heavily referenced by both Sans and Alphys who made a promise related to this connection.
- How Sans and Frisk crossed over to the Neutral Route is unknown, but it is strongly hinted to be connected to W. D. Gaster.