Frisk tells Y/n about a machine that will revive humans.   And that Alphys would have it now.

Y/n took Frisk to Alyphys's lab and entered. They were met by Mettaton.

Mettaton: Hello darlings!

Y/n: I don't have time for you're games. 

Mettaton: Y/n. You know Asgore will be upset when he sees you with a human!

Y/n: I will not allow him to kill another child. If you stand in my way, you will share his fate. 

Alyphys appears.

Alyphys: Y/n! What are you doing?!

Y/n: Doctor, take me to wherever you keep Gaster's machines.

Alyphys: I know which one you want. I don't know if it'll work.

Y/n: Take us to it.

Alyphys nodded and led them to where she kept the revival machine. 

The machine had an input and output chamber.

Chara stepped into the input. The machine automatically started to work.

It was loud and bright. The force that came from the machine knocked everyone but Y/n onto their backs.

The machine stopped and began to smoke. 

Y/n waited and the output opened up. Chara stumbled through and fell to her knees.

Y/n: *softly* Chara.

Y/n ran to her.

Y/n: Princess Chara, are you alright?

Chara felt Y/n's hands, something she longed for. 

Chara: Y/N! *hugs him*

Y/n was surprised but returned the hug. 

Chara enjoyed the moment, but found herself tired.

Chara fell asleep in Y/n's arms, Y/n laid her down on the ground gently.

Y/n: Come, we must get you out of here human. I owe you a great debt.  Asgore might be relieved that Chara lives. But it won't change his resolve.  Not without queen Toriel.

Frisk looks saddened by this.

Y/n and Frisk head towards the barrier.

They reach the throne room and find Asgore.

Asgore: Y/n. I see that you have guided this human through the underground.

Y/n: They have made many friends with monsters, like a few before them. 

Asgore: It does not change what must be done. To free monsterkind, I need one more soul.

Y/n: You shall not have it! I will not let you kill another child for it!

Y/n drew his katana.

Asgore drew his trident.

Y/n looked at Frisk.

Y/n: Stay back. I'll do this for you. You've done me a great service. Seeing you befriend monsters, even Undyne. You gave me hope for humans and monsters coexisting again. I will not allow Asgore to kill you, like I did so many others!

Y/n charges for Asgore who dodges a slash.

Asgore goes for a stab which Y/n dodges and slashes.

Asgore blocks and goes for a slash. Y/n ducks under it and kicks Asgore away.

Asgore shoots fireballs at Y/n, Y/n returns it with arrows.

The projectiles destroy each other. Y/n appears from the cloud of smoke that came from it and slashed at Asgore who blocked and kicked him away. 

Asgore's eyes flashed blue and orange in a pattern, Y/n memorized it and dodged the barrage of attacks that followed. 

The two could have battled for awhile. But suddenly a familiar voice was heard.

Toriel: That is quite enough, you two!

Toriel appears next to Frisk.

Asgore: Tori?!

Y/n: Queen Toriel. *sheaths blade and bows* 

Toriel: It's nice to see you again, Y/n. I'm glad that you decided to defend this human.

Asgore grew angry.

Agore: I won't let this happen. I'm so close, I won't allow this!

Asgore gripped his trident. Y/n jumped next to Toriel and drew his blade.

Y/n: I'll protect you both!

Toriel: Don't worry about me! Protect Frisk!

Y/n: As you command.

A familiar voice once again appeared. 

Chara: MOM,DAD! STOP!

Toriel and Asgore froze. They turned to see Chara.

Asgore dropped his trident on the ground.

Toriel and Asgore: *softly* Chara?

Chara: *smiles awkwardly* Hi. I'm alive again.

Toriel and Asgore ran up to Chara.

Toriel: H...How is this possible?!

Chara: It's hard to explain. But I'm here now. So please, no more fighting. 

The family shares a hug. 

Frisk's friends start to show up. Y/n let his guard down, a mistake.

Suddenly him and the others are grabbed by a large vine. Only Frisk and Chara avoid the vine. 

Flowey appears.

Flowey: Hello, Chara. Welcome back. I'm glad to see the genocide didn't go to waste.

Chara: Asriel! Let them go!

Flowey: While Y/n was fighting Asgore, I absorbed the human souls. I just need one more to become god.  I think you've shown that everyone in the underground can substitute one.  So let's have fun, shall we?

With that, all the monster souls were absorbed by Flowey and Asriel was unleashed.

Asriel: It's time! The end is here!  But don't think this will be a simple one on two. This is a two on two.

Y/n appears with a distorted face, no features were visible with a static screen like appearance. 

Asriel: *sarcastic* I know you'll love this Chara.

Y/n rushes at Chara who dodges a slash. Chara forms a knife in her hand, but finds herself hesitant. 

Chara: Y/n! Snap out of this! I don't want to hurt you!

Y/n didn't respond, instead he kept attacking. Chara dodged every attack while pleading with him.

Suddenly a blue soul went into Y/n.

Y/n heard a voice in his head.

?: Y/n.

Y/n: Matsume?

Matsume: Y/n. Don't make the same mistake.  You want to protect the innocent, so don't let two innocent people die.  You wanted to stop Asgore, but now something worse has taken his place. Take responsibility for this and end this. 

Y/n: I...can't.

Matsume: Tell Chara that. Tell everyone else that you can't. 

Y/n stayed silent inside his own mind. Until he knew what needed to be done.

With a shout, Y/n broke free. He looked at Chara.

Chara: Y/n!

Y/n smirked and ran off to Asriel.

Y/n ran in front of Frisk.

Asriel: H...how?!

Y/n: Prince Asriel. I will not fight you.

Asriel growls.

Asriel goes to slash Y/n who just stands there.

Y/n takes the damage. Y/n is not dead but loses a quarter of hp. 

Asriel: You didn't dodge! Why?!

Y/n: I will not fight. We're friends.

Asriel: You all abandoned me, left me to be a flower!

Y/n: No. We don't have a way to help you, I'm sorry.  But this isn't the way.

Asriel tried to slash again, but found himself embraced by Y/n.

Y/n: It's alright.

Asriel began to tear up as he dropped his weapons and cried into Y/n's shoulder.

Asriel got smaller and smaller, until he was in his kid form again.

Matsume left Y/n and floated around. 

The two let go of each other and stood up. 

Asriel: I'll release everyone and break the barrier.  

Y/n: No matter what happens, I will find a way to fix you. I promise. 

Chara: Maybe I can help. I still have some energy left over from being revived, I don't know what else to do with it. So, maybe it'll keep you this way.

Asriel: Let's do this together, Chara!

Chara nods and the two break the barrier.

Asriel releases everyone and Chara uses the remaining soul energy to keep Asriel in his true form. What she doesn't realize, is that all that energy is from Y/n.

The veteran of the war has so much energy from killing humans, it made him into what he is today.   He was strong before, but each kill made him stronger.

But everyone is free now.  And with that, much more work needs to be done.