exactly the same way you would in diamond or pearl , you have to get a digger drill go to a wall and drill a hole and there you will have your under ground base but i think you need to talk to the old man in eterna city first and do his missions
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first you need a underground kit from eterna city and do some kind of tests until you get to the test where you can make your secret base.
you cant catch it anymore
no
you get a digger drill from an old man in a house next to the PC or you can buy it from hikers for about size 11 spheres
all you have to do is buy a digger drill from a dude and then go to the wall of the place you want your base to be and then go to trapps and click on digger drill its as simple as that