"...a Valiant effort, Mongrel, but ultimately, a shameful display." 

It appeared that Stein, despite his knowledge and supposed understanding and preparations he took against Fragarach, ultimately had not understood how the device worked. When the concept of the weapon was "it would strike the heart," it did not mean it would be an attack on the heart. It was not a physical strike. It was a concept. It was a law of cause and effect. Much like Gae Bolg, which reversed cause and effect to strike, Fragarach struck Stein's heart. A physical defence? Attempting to catch it with his palm? Laughable. Fragarach did not rewrite events to say "it launched itself at Stein's heart before he could launch his strike" and left it open to being blocked. Fragarach rewrote events to say "it struck Stein's heart before he could launch his strike." 

Stein's mistake was believing that he could defend himself from it. The moment he launched his strike, it was over. Fragarach rewound reality itself to the moments before Stein struck, and rewrite reality so that it had imbedded itself within Stein's heart. 

As Darkside carried off a dead Stein, Gilgamesh let out a deep sigh. It had not been a bad day. It was not a boring day, to be sure. This mad beast had shown him power he had genuine reason to fear, but ultimately, no matter how powerful, it could not strike the king. 

Seeing as darkside carried off Stein's corpse, Gilgamesh disappeared, returning to his spiritual form and left.