From Destinypedia, the Destiny wiki
The Garden, as it is referred to by the Darkness, is a metaphor for the probability space from which all possible universes could arise, a mathematical structure that predated time, space, and existence in general.
In the metaphor, the garden was a simulator, using the flower game as a mechanism to iterate different potential universes. This game was overseen by abstract mathematical principles personified as a "Gardener" and a "Winnower". The gardener represented the rules that allowed flowers to be placed, to spread, and to sustain themselves over each "tick" of game time, while the winnower represented the rules that culled flowers.
Playing the flower game, the gardener and the winnower iterated an indeterminate number of potential universes. However, while any number of universes could be simulated in the flower game's patterns, every one was inevitably overcome by the same "final shape", which would repeat itself endlessly across the board and subsume all other patterns. While the winnower admired the ruthlessness of this dominant pattern, it frustrated the gardener, as its all-consuming nature prevented other possibilities from arising and limited the scope of the game. 
At the end-state of one such simulation, the gardener proposed inserting a new, parallel rule to the flower game that would reward difference and complexity, curtailing any one pattern from overtaking the entire board. Their proposal alarmed the winnower, who feared that the gardener's rule would generate malformed patterns that could not be culled, corrupting the game. Undeterred, the gardener inserted themself into the game as the new rule, in the process establishing that changing the rules of the game was a valid rule and so making the winnower a new rule as well.
Metaphysically unable to respond in any other way, the winnower used their new power to attack the gardener directly. As the two fought, they devastated the garden, and real universes, no longer simply simulations, coalesced out of the damage they inflicted to it. Disastrous perturbations in the probability space were translated into Big Bangs, symmetries, and laws of physics. The final shape (no longer inevitable, now that the rules had changed) and other abstract principles native to the garden fled from the conflict and into the multiverse.
Eventually, the winnower defeated the gardener. However, with the flower game over, and the cosmos now real, immutable, and irreversible, their victory in the garden meant little, and the two moved their conflict into the multiverse, to determine its ultimate fate.
List of appearances