<As the first word of the title states, this is merely an attempt. This is a summation of all we know about the Traveler and Darkness when it comes to their history together.
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[b]- Sometime[/b], either at the beginning of the universe or shortly after, Light and Dark entered our universe. Not the one we all know, but paracausal forces beyond comprehension. Whether these powers created, or are merely wielded by the Gods of Light and Dark, we don't know. There's even a possibility that the beings created their powers.
There's another possibility that they came from the same power before splitting apart, as some sources suggest that Light can be turned into Dark and vice versa.
Because of the conflicting nature of the two Gods, the Light being giving and helpful and the Dark being simple and a living force of entropy, the former was hunted by the latter.
Also, the Traveler's mere existence messed with the natural order, and it's implied that it spawned or had a hand in creating or tending the Black Garden. It is not responsible for its Heart, though.
[b]- Pre-Fundament[/b]. At some point before the events of Fundament, the Traveler visited the Harmony and actually managed to finish its rounds there, leaving behind the Gift Mast. The Gift Mast warps Harmony's black hole and radiates Light, making it the only known record of a second Light source. This event was placed before Fundament because the Traveler's been on the run since then.
[b]- Fundament[/b]. The Traveler actually managed to seal the Deep in Fundament, or at least one of its client races, the Worms. The Worm Gods (Akka, Yul, Eir, Ur, and Xol) were guarded by the Leviathan, a massive creature empowered by the Light and possibly the inspiration for Calus's ship (see I Am Alive). In case they made it to the surface, the moons were inhabited by the Ammonites. The Ammonites were cephalopods who directly benefited from the Traveler's work.
The Worms used their power to draw in other species to Fundament, causing entire planets to crash into the gas giant's oceans. One of the species to arrive on Fundament were the Krill, more commonly known as Proto-Hive. After one of their kingdoms, the Osmium Court, fell, the three heirs to the throne came across a derelict ship and a dead Worm still capable of speech. They dove into the planets ocean, avoided the Leviathan despite its pleas, and made a deal with the Worm Gods themselves.
As the Hive started their crusade, the other species of Fundament were put on high alert. The Leviathan was driven out, killed, and fed to the Worm Gods. The Ammonites were extinguished and the Traveler fled, starting the chase once more, this time with the Hive involved.
[b]- Post-Fundament[/b]. We don't know much about the two paracausal forces during this time. At some point, the Hive took down the Gift Mast. Before then, the Darkness annihilated a fortress world. It's unclear when the Darkness gained the pyramid armada as its personal fleet, but it seems that this period of time is likely, as it would be difficult to trap hundreds of ships and the Darkness went undefeated until the Collapse.
The last event of this time period was the Whirlwind, the destruction of the Eliksni homeworld. The Traveler arrived and gave them their own Golden Age. They then promptly had their own Collapse. While many of them managed to evacuate, it didn't stop Oryx and maybe even the Darkness itself from throwing them into their own dark age. The Traveler left the Eliksni as its enemies arrived in the system.
[b]- Sol[/b]. Between what's presumed to be 2013-2020 AD, the Traveler arrived and began terraforming the Solar System, starting with Jupiter's moons. For an unknown reason, it stopped and moved to Mercury, then Venus, then Mars. It was intercepted on Mars by Ares One, where its existence was proved to humanity. The Golden Age began shortly after, which renovated humanity as a society (North American Empire represent) and gave us some dope technology. This tech included programmable matter (Glimmer), self-replicating/powered nanites (SIVA), robots (Frames), human robots (Exos), and the ability to start colonizing and terraforming other worlds without the Traveler.
Towards the end of the Golden Age, the Traveler moved to Io and began its process. The colony of Titan found a Deep Space Anomaly and sent probes to investigate. Whatever was out there scared them so much they evacuated en masse soon after, the Traveler also leaving Io half-finished, retreating to Earth.
The Darkness arrived and began destroying everything. The fleet spread across the system to cover every major installation, which is why we have accounts pointing towards simultaneous attacks on Earth and the Reef, and definitely more than just those places. The Collapse ended when humanity exhausted all efforts to hurt the Darkness and the Traveler released a burst of Light. The ensuing battle left the Darkness defeated (and potentially its God dead) and created a new (possibly two) human subspecies, the Awoken. The pyramid armada left for the galaxy's edge and the Traveler fell dormant.
The Traveler, in its last moments, released the Ghosts. These drones started seeking out individuals capable of wielding the Light. While Risen started out as a shaky concept art first, many of them joined humanity's remnants under the Traveler as Guardians, the second-most powerful group of people in Destiny's universe.
Some remnants of the Darkness remained across the galaxy. Before the Red War, the Drifter and his crew flew out of the system to an ice world which held gooey black creatures that were equated to a living Darkness Zone. While some were frozen in monoliths, most roamed the planet freely, even when the Light shut off when Ghaul took the Traveler.
Another example of a Darkness-borne entity finding a new home after the Collapse is the Aphelion. This entity is responsible for the murder of many Techuens, the attempted murder of Sjur Eido, and the deaths of 300 Awoken aboard the Amestris station. Regarding the latter, there were no signs of malpractice, malfunctioning tech, forced entry, struggle, anything. There were only lethal levels of radiation and no survivors.
[b]- The Heart, Bait or Failure?[/b] The Black Garden got a new addition, the Heart. The Heart of the Black Garden was either a Worm or Shard of Darkness that was put into the Black Garden. Its presence there kept the Traveler from healing, but didn't do anything else. The Vex attempted to use it to empower the Sol Progeny, three Vex Minds meant to be real-world Atheons. Their attempts were foiled by the Young Wolf and the Black Garden was plucked out of space-time and stuck on Mars.
The Heart's origin is the only thing really unknown about it, and that knowledge is critical to determining what the Vex had in mind with it vs what it was supposed to do. One theory is that it's the Worm that Quira took from Oryx's Throne World. If so, the Heart was a failure all around. The other theory is that it's a Shard of Darkness. How the Vex procured it, if they did at all, is unknown. If they didn't take it, then it was put there by something else. If that's the case, then Uldren's theory isn't so crazy.
If he is correct, then the Heart was meant as bait to attract Guardians in order to determine how strong the Traveler was getting. Its destruction would tell its masters what to do. This means we would've been feeding the pyramid armada data about our strengths, which gives them time to determine how hard they want to hit Sol and how to exploit our weaknesses.
[b]- The Red War[/b]. Ghaul came into the system (thanks 1 of 9, you asshat) looking to take the Light. He shut the Traveler's power from all Guardians until the Young Wolf was picked out by the Gardener herself and got the Light back. Ghaul did manage to take some Light for himself, but upon realizing the extent of his power and gloating about it, the Traveler woke up and absolutely shredded him in seconds.
The burst of Light that reached out across the universe hit the pyramid armada and they were re-activated, beginning their journey to Sol once more. More and more individuals began hearing of their imminent arrival, such as Mara Sov, Toland, the Drifter, Calus, etc. Some of them began preparations by setting up trials (Drifter - Reckoning/Nine - Trials of the Nine).
[b]- Shadowkeep[/b]. Somehow, the Black Garden was ejected from Mars and thrown into space. Considering its nature, it is unclear who/what did this, but it did this for a reason. The pyramids draw ever near, getting closer and closer to their destination, but they won't arrive now, it is not the time.
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That's all I got so far. The Darkness is coming back, and we will not survive it this time... or we will because plot, but we'll get our asses kicked.>
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I have to disagree with the possibility of Calus' ship drawing inspiration from the Leviathan. The ship is modeled after aquatic creatures on Torobatle that routinely beached themselves and ate cities in Torobatles past. There is evidence in the literature provided in the Collectors Edition of D2, I think there may be some in the Lore as well.