Harvest Moon GBC3 has two parallel plots, based on which gender the player picks to play.
Pete: The boy from Harvest Moon GBC 2 in Flower Bud Village has made a success of his farm. Mr. Heinz, the mayor, tells the player about a friend of his that lives on a far away island. He says that this friend has died and now his daughter is going to take care of the farm. The girl doesn't know the first thing about farming so Mr. Heinz asks you to help her get the farm started.
Sara: When playing as a girl, you start as someone who used to live on an island with her father, Harry. A while after leaving the island, you receive news that your father has died, so you return to look after the farm. Mr. Heinz enlists someone from another place to help you work on the farm.
Harvest Moon GBC 3 has a partner system that sets it apart from other titles. There are almost two games depending the player's chosen gender. Girls take care of animals, and boys manage crops. At the beginning, the player may need to fulfill both roles, but as the partner grows fond of the player, they become more efficient at their work and will require no help. You get to choose Blood type, which is another unique feature.
The gender-based roles on the farm define the tools the player can use. Male players have farming tools that level with use, but no access to tools related to the care of animals like the brush or milker. They must rely on their female partners to gather milk and wool. While female players' tools will never level up, they have full control over the animals and have the ability to buy Shampoo to care for sheep. Male players cannot buy Shampoo and their partners will not have it either. Female players must also buy machinery to make butter, cheese, yarn and sweaters, while the male player can teach his partner the ability to make these items by hand from books at the mall. However, he has no control over what the female partner will make (or when).
Finally, marriage, which is the end of the game for players on the girl's path. The boy can continue after marriage and have children. Though the farm life is defined by gender, the game has two maps for different areas - the Island map, and the Mainland map. Both have a few different activities and events to experience.
In this game, players can:
- Get married
- Have part-time jobs
- Own eight of each animal
- Use a boat for ocean fishing
- Sell items at a market stall
- Play a snowboarding minigame
- This is one of the few Harvest Moon games to be released in Europe before America.