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I think UB-01 (along with any other Ultra Beast) was artificially created; most likely by Aether, though I can't surmise their motive without more information. Looking at its design, it's obviously connected to Lillie in some way, but how? It's possible that the creature and Lillie are one and the same, but that raises countless questions. Why does UB-01 take the form of Lillie? Why has she been assisting Professor Kukui? What is the thread connecting Lillie to Aether, and to UB-01's design?
It's impossible to make any educated guesses with what little there is to analyze, but I have my own theory. As others have pointed out, it's not crazy to think that Lillie and Luminose, Aether's president, are somehow related, perhaps by blood. What if, rather than Lillie and UB-01 existing as one entity, the beast was simply designed to resemble Lillie in appearance? I suspect that out of love for Lillie, Luminose and her team created UB-01 in her image, with some sort of righteous goal in mind. But perhaps something went wrong, and now it presents a threat to humans and Pokemon both? Again, it's difficult to hypothesize without more information, but I feel that human experimentation may be a touch too dark for a Pokemon title. Unless others are correct in presuming that UB-01 is an entity from beyond, taking Lillie's form and simply being researched by Aether. Who can say?