After beating up Hector on top of a cliff in the Everfree Forest it was a losing battle, Henry's smallpox disease made him weaker, and weaker, and as he was about to reach his Revolver to kill Hector, and save Canterlot, and couldn't make it. He did not only die from his disease, but Hector beat Henry to death which is the real cause of his death. so in the Epilogue Henry and Pinkie's son Tony Santos, gets his revenge for the death of his father, 18 years later.