Ōkami has the final boss Yami, who doesn't seem to look remotely evil, and his forms seem to just be an addition to his power, until one realizes his forms are the evils humanity has performed, Destruction, Burning, Gambling, Energy being used for evil purposes, and the hand of which does this evil, some people either interpret Yami's True form, a fish, as being an ironic evil, or things start out innocently enough, but then everything goes bad. So Yami's not so much a sign that Science Is Bad, but those who would use it for evil purposes. —Etheru
The line about the fish-thing (seal fetus?) inside Yami can be taken further: the fish represents a person (or possibly nature in general) being surrounded by the negative aspects of humanity and thus being twisted into something evil. It's basically innocence being corrupted by the evils of humanity. Why else would it be a small thing almost always surrounded by Yami's different forms? And Amaterasu having to attack the fish-thing to lower Yami's HP represents destroying the corruption.
Alternatively, Yami can be seen as what happens when science goes too far. Without going into very detailed biology, at some point in the human embryo's development, the fetus looks roughly like a fish. So Yami could very well have been created with good intentions, however eventually it became corrupted. A bit of a stretch, but that's how this troper sees it.
When you explore the sunken ship with Rao, you come across seals that require you to guide Rao's power to dispel. It seems like a gameplay and story segregation function allowing you complete control of story progression. The brilliance comes in when you realize Rao doesn't have any holy power, since she's a major demon. You are using the real Rao's tools as a conduit for Amaterasu's own holy powers. It's not just that the fake Rao doesn't fight enemies or cursed zones herself, it's that she can't- or at least, not without giving herself away.
Remember the prayer slips Rao used when you were on the ship? Tobi looks the same as those, doesn't that tell you a lot about "Rao".
The theme that plays during the second part of the final boss fight with Yami is called The Sun Rises. Considering that Amaterasu is the sun god and, and that Japan is called the land of the Rising Sun, the song is basically saying that Ammy is taking back her world from Yami.
Praise is used to level up your health and ink capacity, at the end of the game you receive praise from everyone in the game, and get levelled Upto Eleven
Regarding Yami's first battle theme- on the OST, it usually lasts about seven minutes. The maximum length of time a solar eclipse can last? About seven minutes!
Okamiden: While traveling through the Goryeo, Chibi encounters a sailor who is managing a fish tank which contains a shark and, apparently, some crabs. Now who are the bosses of the Sunken Ship? A pair of crab demons who fuse into a shark demon.
Okamiden: Near the beginning of Okamiden, Susano says that he knows Chibi. At first, you think he's mistaking him for Ammy, but then Chibi and Kurow find him outside of the Moon Cave when he was going in to slay Orochi in the first game.
In Okamiden, instead of ink trailing from Chibi's tail, it looks more like a crayon or charcoal. What do kids like him love to draw with?
For Ōkami, there's Yami. Yes, he looks harmless, even with his armor, but consider the fact that he has weapons that people didn't have access to at the time, put yourself back into that age, think about what happens when Yami wins and pretty much destroys the world...
Blight is made of swords. And lives in a Womb Level. It sucks to be the Emperor.
The giant seaweed monster from the sunken treasure ship gives you a ton of praise for killing it. The praise is coming out of the monster its self and not from the surrounding areas like it usually does when you take out a demon gate or other large monsters... It wanted to die.
It's made even creepier when you consider what happened to the ship in Okamiden where most of the sailors died. That giant seaweed creature was probably an amalgamation of their souls being stuck there after death.