The Megalith are currently the looming threat over the Cartoon Network Universe. It is so far known that they have invaded the earth once before, leading to the creation of Project Exonaut. It was how to deal with them that led to the Civil War amongst Exonaut Academy.
So far in the game, it is unseen and currently it is unknown whether they are organic creatures or machines. Fortunately, it is known that Project Exonaut creators have "plans" for their appearance.