Okay after you first enter the base get past the first camera followed by two grunts, go for the first opening/doorway or whatever you want to call it & proceed. Possibly followed by one more camera and enter another close by opening then follow the path leading to a room [with 2 plants, and a scientist, and some item(forgot what it was)]. After defeating the scientist approach the computer and press "a" and select "yes".
Or if you feel like it you could train your Pokemon by battling grunts(optional).
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