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it seems that there is one big invisible mothership, and a few little drones which appear as lights. the mothership uses somekind of stealth technology to reflect and refract the light so it gets invisible. but when the mothership is moving a bit, it is possible to see its structure.
at another time in the movie, a man, alien or something else, appears on the mothership or behind it (or somewhere else...). then the alien or what it is, walks into the direction of the lights, kneels down, and then runs (very fast) away.