Meta Battle Subway PokeBase - Pokemon Q&A
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When I go into a Secret Base I find the flag next to a computer, I take them but... what do they do?

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Your Flag collection, as it gets higher, allows you to buy more advanced equipment at the Secret Base shop in Fortree City. At 30, you reach Bronze rank, Silver at 100, Gold at 500, and Platinum at 1,000. At each rank-up, you get a reward.

Secret Base Guild Rank Rewards:

Bronze Rank - 30 Flags - Blackboard

Silver Rank - 100 Flags - Jukebox

Gold Rank - 500 Flags - Mood Lighting

Platinum Rank - 1,000 Flags - Confetti and Garchompite

Note: You must talk to Aarune after you've collected enough flags to rank up, you do not rank up automatically.

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it also affects how many abilities your secret pals have available for you to use
Also true