John doesn't comment on it often, but Mike Portnoy opened up in an interview about why it was written and what he thinks it's about. In the interview, Portnoy was very careful to remind the reader that he could be all wrong, but that it was not likely.
Petrucci wrote it as a sort of Twilight Zone story about war, in which the main character witnesses all these atrocities and sees the names of the dead on a wall. He then realizes it had been him the whole time causing the atrocities... then he sees his own name on the wall.
This man wakes up in the middle of a field with a wall full of names, names of the dead. Seeing this horror he tries to find a way to go back in time. For whatever reason, which John himself doesn't really know, the way to go back in time in this universe is to go to the bottom of the Ocean, which he does.
Arriving in the past he sees a dictator ruling over the land with absolute cruelty, the Killing Hand. He begs the spirits for his body and soul to be materialized at that moment and it is, he then stops the Killing Hand.
After this the sea calls him back once again, because his time is up and his spirit must return, and it does.
He goes back to the valley with the writting on the wall and looks at the names, no one is left out from before, and there is another name, his name.
He is the Killing Hand.