For the most part, each plant may only be planted in one particular season, and if, for example, a spring plant is in the ground during summer, it will die.

Once the seeds are sown, the player must water them daily, and after several days of growing, they will be able to be picked and either sold, given away, eaten, or stored. In the beginning of the game, the player is given a farm littered with rocks, stumps, and various objects littered throughout. Each type of seed has a different growth rate and cost, and some plants can be harvested multiple times. The player begins with two tools, the hoe and the watering can, allowing the player to till the land and grow various plants after the player purchases or obtains seeds. The weather varies from day to day - while it is typically sunny, there are occasional rainy days, and, rarely, storms might damage crops and force the player to stay indoors. All four seasons are included, though there are only 120 days in the year, with 30 days per season. The game runs on its own clock and calendar while the player is outside, one in-game minute passes every second. Rune Factory 2: A Fantasy Harvest Moon has gameplay similar to its predecessor. The bottom screen of Rune Factory 2: A Fantasy Harvest Moon shows the protagonist battling an enemy in a cave, while the top screen shows a map of the location.

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