I saw this anime movie in the 1980s and I am pretty sure it was new then (but I could be wrong). Humans have colonized the Moon and discovered an abandoned alien base in the process. I never saw the whole story, so I don't know if the aliens ever returned - what I did see was human political intrigue over who controls the base.
Might this be Dallos?
Released in 1983, it features a human colony on the Moon who discover a mysterious structure, resembling a giant face staring up at the sky.
It was a four-episode series, but they were also edited together and released on video as a movie.
Decades ago, the moon was colonized and turned into a mining colony whose profits benefited Earth and its people. A generation has passed and the workers are now treated as slaves -- forced to work in the mines under the rule of earth-born men, with many of the young people having never been to the land of their heritage. The time has come, however, for a rebellion to take place: to command Earth to hear their pleas; and afterwards, the moon and Dallos, the moon's god-like structure who silently sleeps and protects its inhabitants, will never be the same...