Furthermore, these "higher beings" may not be omnipresent or even omniscient. These "higher beings" are just as the name suggests, higher, more advanced, morally, technologically, cognitively, etc. in comparison to the "new beings", hence the "destiny to help a new generation of beings...". (I mean the NSA is omnipresent, aren't they?) So it's quite possible that these "higher beings" may just have advanced technology, that the "new beings" don't understand and see it as "the powers of the gods".
Although, of course, the "higher beings" may not intend to help and promote the "new beings" but do so by accident. If the "higher beings" have become advanced enough to travel through the vastness of space, but have yet to "...find all the answers" and become truly omniscient, and they happen to land on a planet with primitive beings. Then the primitive beings, or "new beings", see these foreigners as "the gods coming down to visit them". In turn, the "higher beings" could potentially have a great influence on these "new beings" and could even push the "new beings" technologically and morally more quickly than they would have alone, all without meaning to do so. And these "higher beings" could either use this situation to help the "new beings" advance or just use the "new beings" as slaves or as disposable pawns on the chessboard. However, the "new beings" might not understand the purpose of the "higher beings", so they would see their actions as "god's will" or "the might of the gods". More so, the "new beings" also might not understand the expanse of the technology of the "higher beings" so they would describe them as they saw and in the way they understood. For example, a modern day plane may be titled "the Great Bird of ____ - the God of Fire" or something of the sort.
As a side note, feel free to comment on or question this theory, because after all it is just a theory, as of now. And this theory is far from flawless, so if you notice any significant holes, let me know and I will try to answer them.
This has nothing to do with April Fools...