In the Neutral Route, Clover never fully commits to any form of Justice. At the end of the game, instead of fighting Asgore, Clover decides to give up the mission and live a peaceful life with Martlet. Flowey suddenly appears, killing her before this can happen, and sadistically tortures Clover until he gets bored. Flowey resets time to start all over again, with a strict command to go to Asgore next time.

In the Pacifist Route, Clover decides to kill no monsters during his approach to Asgore, attracting the malevolent attention of Ceroba, who secretly needs the Soul of a pure, nonviolent human to complete her late husband's research project - a serum that will allow Monsterkind to defeat humanity in a future war. She proceeds to manipulate Clover into seeing her as a friend and ally, only to act as the route's Final Boss when her ruse is eventually discovered. After Clover defeats her, she surrenders and asks to be killed for her crimes, allowing the player the choice to kill or spare her before they move on to Asgore, with each choice yielding a somewhat different ending: either way, Flowey allows Clover to die, resulting in Asgore taking his Soul.

In the No Mercy route, Clover kills any monster that seeks to oppose his approach to Asgore without mercy, acting as judge, jury, and executioner. Empowered by violence, Clover overrides Flowey's control of the timeline through sheer Determination, allowing them to kill Flowey. Clover storms the castle, kills Asgore, and then leaves the Underground with the 5 human souls in hand.