The theory that the Earth was born moonless and was hit by a Mars-sized plant, ejecting into space material that became our moon does not explain why the far side of the moon is so different from the side we see. Some researchers say our planet once had two moons. The missing satellite might still be up there. The competing theory says our two moons joined in a slow splat, with the missing moon becoming the far side of the Moon that we see now. The GRAIL mission data was going to look at the two moon theory by examining the gravity differences inside the lunar orb.
NASA's moon-orbiting GRAIL (Gravity Recovery and Interior Laboratory) mission measured the lunar crust and confirmed that it's thicker on the far side; the spacecraft also found that the near side (and the near side only) has a network of long, linear, buried features, which planetary geologists interpret as volcanic dikes.
Linear buried features? Looking under the surface of the moon, the GRAIL mission saw this:
Another striking feature of Ship Rock are the dikes, or wall-like sheets of lava that radiate away from the central neck. A total of six dikes have been recognized. These dikes would have been intruded at some depth below the earth’s surface at the time that the Ship Rock eruption was occurring. Like the neck, the dikes have since been exposed due to differential weathering through time of the hard lava of the dikes, and the more easily eroded sandstone and shale of the countryrocks.
So, not a secret alien underground base, most likely. But did the earth have two moons? The idea is still unproven.