This is how I would imagine Celestia within an Undertale-style MLP-game:

In all routes, like the different neutral ones and the pacifist one,

Celestia will never fight you. She will always try to talk to you, even if you

harm her. She will be forgiving, even if you have done some really bad things.

Because she is a pacifist herself and believes in redemption, she will let you

even kill her, instead of fighting back.

In all routes, except genocide…

When you have killed everypony, when you have shown no mercy to any creature

that crossed your path and when you have made an EFFORT to get even the last soul

in Equestria, then Celestia will lose her nearly infinite patience.

Additionally, with nopony else alive, she has no reason to hold back anymore…

…and then you will have a really bad day.

The fight would work like this:

Celestia becomes as hot as the sun and if even a single one of her fiery attacks touches you,

you die.

You also can’t attack her, because when you touch her, you will vaporize as well.

The only thing you can do is survive. This final battle is a “no hit”-fight.

You must memorize the attack patterns and you will most likely die a lot.

Celestias power output is enormous. That means that she can’t hold it up forever.

If you survive long enough, she will eventually run out of power.

Once she has no energy left, you can attack her until she dies.

But even then she will still fight back by attacking you with her horn, eventhough

her attacks become slower and slower (a bit like when you kill Undyne in a neutral run).

Well, that are my thoughts.

I would be interested in hearing your ideas, especially for other characters! :-)