46 Okunen Monogatari: The Shinkaron (which translates to "The Story of 4 600 000 000 Years: The Evolution Theory") is an unusual role-playing game that puts the player in control of an evolving creature. The playable character is a fish at the beginning of the game; after completing the "fish stage", it becomes a reptile, and so on, until the highest stages of evolution are reached.

Despite this premise, the game retains elements of a "regular" story-driven RPG, with an overarching narrative (the player character is a creature chosen by the goddess Gaia to evolve and protect the Earth), and quest-based structure. The animals in the game can talk to each other, it is possible to chat with friendly NPCs, and the game advances once certain quests have been completed.

The player navigates the heroic creature through (mostly) top-down areas. Hostile creatures are visible roaming the environment. Whenever the player-controlled character touches a hostile creature, a turn-based battle ensues. The battles are viewed from first-person perspective; the player can attack, use special abilities, or flee. defeating enemies awards "evolution points", which can be distributed to increase the playable character's parameters.

Unlike most Japanese RPGs, 46 Okunen Monogatari allows the player to upgrade any of the four main parameters manually, in any order. These parameters are: attack power, defense, intelligence, and endurance (needed to reduce or eliminate damage received from certain terrain types). Once one of these parameters "levels up", the player-controlled creature evolves into a different, stronger one. The evolution tree for each animal type is rather small, but non-linear, i.e. the player can bypass certain types depending on how he/she builds the character.

The game offers exact descriptions of the animals the hero can turn into, and re-creates real prehistoric evolutionary trees.

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