The light spirit Aska was captured by Thor a long before the game took place. However, the civilization had to contain him, paralyzed, because they lacked the technology to experiment on a spirit. Before they could develop this technology, the comet Samier crashed into Thor, plowing it miles into the ocean. Thousands of years later, the city surfaces thanks to the intervention of the player. The player now can go on an optional side-quest to free Aska.
As a result of Time Travel there are two versions of Dhaos imprisoned at once which indicates that tampering with the timeline results in changes you want and that things you expect to be the same will be unchanged.... What is the likelyhood that their's an alternate version of Cruxis ruled by a time traveling megalomaniac waiting to make it's move to conquer Aselia?
Remember what the substance used in making Rune Bottles does when used on some items (such as gels and herbs)? Turns out it can be (and might have had been) used on monsters, too. Just take a look at some monsters encountered only at the Coliseum in Euclid and nowhere else. Put two and two together and you'll realize these monsters may have been subjected to not just captivity, but also biological experimentation of sorts, too. While not explicitly elaborated upon in-game, this somehow counts as Nightmare Fuel.
In one of the end-game sidequests, a man named Grahan asks you to find a series of treasures his father, a pirate, once hid all over the world. You can keep most of them, but there's a special one you have to bring back to him. Turns out it's his mother's wedding dress and Klarth comments that Grahan's father knew what the important things in life really are. Likewise, the reward for clearing this sidequest isn't money or items - it's simply making Grahan happy.