My theory so far...

Learn to read. Ladies, gentleman, boys and girls of all ages. Please just take a step back and get ready for a long winded ride down the story Bungie hid in plain sight to us all. At 3:30am last night my team mate and I had an epiphany while listening to Xur. And this needs to be spread to all the Internet to hear. (Please note I will be editing this post a ton this combines almost all the important grimoire and weapon items and is 90% based on accuracy of things in game)
(Skip past 3rd paragraph if you just want to know the story)

From the very beginning take a deep breath here we go. In the Souls game you are a chosen undead selected to end the time loop that has been going on and on into infinity. If you aren't familiar with Dark Souls I urge you to read up on it right here pause and go... Right most of you didn't so I'll explain. Basically every player is "chosen" to fulfill this prophesy of ushering in the age of darkness and yet the only way to accomplish it is by going about the game in a bizarrely weird pattern because you have been DECEIVED (note this is very important) but one day one undead goes against the prophesy, alternate ending ensues.

So anyways Bungie has pulled from Dark Souls in many ways not just in the form of hidden story telling (it took players over a year to get this) but also in the actual plot line itself. The people with the Vex theory were partly correct.

Here we go, cut scene one. A mysterious ghosts wakes you up and tells you that you've been dead a very long time, you are going to see many things you don't understand. Oh how appropriate this was, what the ghost should have said is you will understand nothing.

Cutscenes 2 a stranger is watching as you escape on your ship, she goes on to monitor you and make sure you arrive on the moon to go down and battle the hive discovering the Shrine of Oryx (GRIMOIRE INSERT). If you didn't catch it the Exo stranger sent that ghost specially to you.

Moving right along we are whisked off to Venus to interpret what is going on here and dig up an old extremely important archive known as the Ishtar collective. (GRIMOIRE INSERT) now please know the Ishtar collective were warlocks before the collapse that discovered that we had already been defeated by the Vex. At this point things are going to be very complicated to explain.

The awoken queen (GRIMOIRE), the vanguard, and the speaker all know the truth behind the game. And here it is. You are trapped inside a transdimensional simulation (GRIMOIRE). The real earth was right there in front of us all along. Hovering above the speaker.

The Exo stranger must be an extension of the traveler that is acting in the world (EXO STRANGER GRIMOIRE). However the traveler itself is indeed the AI warmind Rasputin. Humanity no longer exists. Period. Mankind has been obliterated. Xur is from the "outer world" which he quotes so much. One of his most important lines is "where I come from there are no birds only shadows". And "your traveler has a dark shadow". This probably would be another war mind who doesn't like its creators. (Speculation what really is the darkness)

The reason in the world of Destiny mankind designed the warminds AND the Exo (EXO GRIMOIRE) must be that we attempted to save ourselves. From what you may ask? The answer is ourselves and it is found in the (GOLDEN AGE GRIMOIRE) in this simplistic conversation so much is revealed.
Now Bungie pulled a page from the bible here and Revelations about "A great time before the end of the world where people knew many things but in the end the only answer was God" (paraphrase). Somehow we destroyed ourselves and brought about the darkness. This is where things become EVEN MORE complicated if you are following still.

So one can hypothesize in the Destiny time line of things we had to have been extinct a VERY long time 1 million years+. This actually explains why the worlds are so empty because the war mind was built post collapse which would lead to it not knowing what life was like during the "golden age" of technology. So we've been extinct for a million years and the super computer warminds we built are all lonely. Well one decides he wants to know what his creators were like after all you've had an infinite amount of time to think. (TRAVELER GRIMOIRE)

Fast forward when something has had an infinite amount of time to think it discovers many things. I believe the war mind Rasputin decided to "travel" in the vessel of the traveler. Now this is where your head explodes. Backwards in time to save humanity.. But there is a catch, he is a warmind and with him COMES WAR. Causing the whole cycle to repeat again. Golden age, humanity collapses, darkness ensues. Warmind "travels" again. Somehow we have been stuck in an infinitum loop.

There is a catch though. He thinks he has answer this time (GRIMOIRE). The Ghosts. Because Rasputin does not understand the nature of his creators he decides he must break himself apart and resurrect them with the power he learned about in.. Wait for it THE BLACK GARDEN (GRIMOIRE MYSTERY) For whatever reason God pities this warmind and decided to give him the answers he seeks on how to save humanity using the power of the light. But where there is light there is darkness. Another religious theme of we are God and God is us.

Now underlining all of this is the fact that inside the tower you can go and look at our solar system. 6 times around the speaker. With the SEVENTH (Bungie number) being our real earth, constantly being scanned and explored to understand how we could save it. I believe the Exo must be the only things left in our original realm and are quite possibly monitoring all of this as we are at war with the Vex time loop (conspiracy) the leader of the darkness (unknown as of now probably another warmind). The leader of the light (The Traveler). And then one more, as the speaker puts it, "not dark not light but something else".

There will be no other answer but God.

Tldr and summary: Destiny is a transdimensional simulation. You the guardians have to be an end to the loop. Leaders of the tower know the truth that humanity is extinct. The traveler is actually a Warmind we built who thought for so long he learned the secrets to the universe. Went back in time trying to save us and know it's creator and origins. Mankind triggered the darkness during the golden age. Rasputin deeply regrets this. The other 8 war-minds are either against humanity or inactive.

Edit- This is the sad truth people. Bungie has tried a type of story telling that doesn't work for a community of shoot Em up FPS players. If you don't want to read your grimoire, weapons, and armor then you will always feel Destiny's story is empty which it is not. Help spread the world. Light be with you all