Vogol's Art

You see this is what happened:

Undyne planned to take over the Estate and kill Rin. So Rin sent her top bodyguards, Linkle, Phasma and Sahru on a hunt for her. Phasma found her first.

And shot Undyne through he chest with a high torque crossbow.

She died from the shot.

Kyo came upon the body of Undyne and was sickened by the sight of decaying flash and opted to destroy the body completely, burning it to a crisp.

After the young Kusanagi was done with Undyne there was only a pile of ash that remained.

That was blown away by the slightest draft. 

And that was the end of Undyne’s attempt to topple Rin Aensland…

Funny enough. Some say that Undyne’s ashes were eventually found by Drevio who proceeded to use them to season his wild chicken roast.