I like to think that the traveler is a weapon created by humans years ago and we used it on these other species planets/solar systems for our gain (humans are greedy -blam!-s). And now all these races are attacking back at us for what weve done, this also explains why guardians seem to have no memory of what happened before ( who wants to be told your the bad guy) and also why there are some exos and awoken that seem to be fighting for themselves or a seperate cause because why should they fight what we started (the stranger and the queen).And the darkness is kind of a physical and metaphorical manifestation of karma coming to set everything back into balance. Then all of this is revealed to be "the nines" doing as they are beings who thrive and love when species are at war which is why xur is selling us the weapons and gear to fight back against these odds we face. Yeah so pretty much traveler is a weapon, darness is balance, the nine is evil