In the world of Golem Hearts, creatures known as golems have become integrated with society, performing all sorts of tasks. These golems are created by the widely-respected "sorcery scholars," and obey the commands of their human masters without question. Noah is a sorcery scholar who strives to become the second best of his kind.

To that end, he travels far and wide to study unique golems around the world. This journey leads him to a certain island, where he encounters a girl named Mary and her golem Murray. As the two get acquainted, we begin to discover that there may be more to Noah than meets the eye.