I think you can, but you have to capture your friends flags (using Ds wirless) 10 times (to remove 10 rocks) and 50 times to remove all of them. After you cpture 50 flags talk to the underground guy in Enterna City to remover the rocks
The thing is, there usually is only around 10 rocks.... so therefore, the logic is to capture the flag 10 times...
But there isn't much point to secret bases this time round. The amount of items allocated inside is far too small.