First, let's start from the basic premise: Jason Jones is notoriously bad at sticking with any project for too long. He hates sequels, he hates being tied down to any particular idea, he wants to move on as soon as possible, and he wants all of Bungie to move on with him. This is behavior that has been well-attested to by many Bungie employees over the years, and is a pattern that has gone back to pretty much the studio's founding. It's so bad that he has frequently needed to be tard wrangled into actually doing what they're contractually obligated to be doing.
So, with that in mind, it's obvious that no matter how excited he initially was about Destiny to begin with, he inevitably soured on it and was ready to move on. Why he was okay with signing a decade-long contract with Activision, knowing his past experiences, is beyond me. Maybe he figured this would be the project that would keep his interest for once, but once again, that proved not to be the case.
So when was he done with Destiny? Probably sometime in the lead up to Destiny 2 after its rocky and delayed development or just after its release, that would be my guess. He probably didn't want to make a sequel anyway, and when it didn't have the best reception, that probably cemented it in his mind that it was time to move on. But the studio didn't have anything else to work on at the moment (and there was that pesky contract, of course), so they couldn't just pivot overnight like he wanted. Thus, the incubation projects. They may have been ongoing the whole time or they may have really started around this time, but either way, Jason wanted a new game, and he was going to make it happen one way or another.
There was just one pesky problem, though: Destiny was still a thing, and it was still doing numbers. It's hard to make the argument to switch the studio over to developing a new game when your existing one is doing well. So what's the brilliant genius Jason Jones to do?
(Rampant speculation from here on out.)
My conspiracy theory: Jason Jones deliberately sabotaged Destiny to force Bungie to work on a new game, either directly or through indirectly pressuring team leads. Look back at various decisions that seem really stupid and illogical, and they start to make sense when you consider that the goal was not to improve Destiny, but to kill it.
Let's start with the first one: killing Destiny 3. As presented to the community, this sounded like a decent idea. No needing to worry about your progress getting wiped again, just continuing on with everything still available to play. The scars of the Red War and losing your original Vault still ran deep. Of course, D2 wasn't designed to expand indefinitely, so various shortcuts that would have been taken during development under the assumption that a brand new game would come along and replace it a couple years later would come back to haunt them. This of course led to...
Vaulting content. Again, this was presented as a necessary evil to the community: "the game is too large and unwieldy to keep developing as is, so we're gonna pull out content that isn't being played much anymore." Hand in hand with sunsetting, this was not a popular decision, and as we can see from the player counts over time, it had a noticeable impact on how many people kept coming back, never reaching the highs it had before. But notably, it also didn't kill the game outright; every expansion still had a fair amount of people keep coming back, and player counts remained fairly consistent over the next few years. Even vaulting the Forsaken campaign and another destination in Witch Queen didn't do much to change the numbers, around when Marathon was starting to move from incubation project to the Next Big Thing. So what about...
Just making some absolute garbage content. Originally, Lightfall was going to be the finale of the Light and Dark Saga, and according to devs, the original version was going to be very different from what we got; rumors have swirled that the intent was that the Witness would basically win and force us to flee the system. Even if it didn't go that far, it likely would have had a much more serious tone. Instead, they tacked on one more expansion at the end in The Final Shape, then went and made the woah cool 80's cyberpunk action adventure enby schlockfest that was the Lightfall campaign. From the tonal whiplash to the insufferable characters to the cringeworthy dialogue to the nonsensical plot to the fact that the whole thing felt like a filler story that you could easily cut out and lose nothing...yeah, it was terrible.
Now, did Jason intentionally direct the narrative department to create the worst story possible in order to sabotage the game's future? I'll admit that this is a bit of a stretch, potentially, considering that Jason seems to be a lefty true believer and probably legitimately thinks Representation Matters™. But considering that he very likely has had a hand in meddling with existing stories before (see the Joe Staten debacle), it's not entirely outside the realm of possibility. Still, while the Lightfall story was complete trash, it wasn't quite enough to deal a deathblow to the game, with a lot of people still sticking around just to see the conclusion. And speaking of...
The aftermath of The Final Shape. By this point, Marathon had been announced and was moving closer to release, but Destiny was still persisting. While a lot of people checked out after beating the Witness, there was still a decent amount of people that wanted to keep playing and exploring the world of Destiny. The episodes were generally met with derision, though, with much of their story feeling unsatisfying in some way or another. Gradually, people were trickling away, but the playerbase was still strong enough to keep chugging along. It really needed a death blow to justify giving it the axe, and thus we get...
The Year of Prophecy. This shit had all kinds of decisions made that pissed players off to no end: killing the Director in favor of the soulless Portal, a massive and tedious power grind for no reason, the continued death of crafting in favor of an endless loot chase, confusing systems that made it feel like you were spending more time in menus than playing, campaigns and destinations that definitely weren't the top of anyone's list, and a lot of radio silence from the people nominally in charge. Meanwhile, devs were getting moved over to salvage Marathon and get it out the door in time, resulting in slower updates for Destiny with less content in them. The results were clear: after one too many bad decisions, the playerbase had finally had enough and for the most part left until things eventually got better. After all, we're used to the Destiny cycle: they fuck up, we leave, they make positive changes, we come back.
Only that's not how it played out. Instead, Jason finally had what he wanted: an excuse to kill Destiny once and for all. Nobody would question the decision to axe development of a game that looked to be on its last legs, after all. "Clearly we tried, but nobody wants to play it anymore!" he could argue. Never mind that the reason people kept leaving was because of all of those retarded decisions piling up over the years (I didn't even get into things like the F2P decision or the seasonal content model or various delays over the years); all the suits actually care about is numbers, and the numbers say that Destiny is a dead brand. Even if Marathon was a total flop out of the gate and doesn't look to be improving, it was still easier to argue that there was more potential in a brand new game than to try and salvage the stumbling old one.
I don't think Jason was quite prepared for the blowback, though. As soon as the announcement dropped, fans both old and new were in an uproar. Months of nothing from comms only to have the game unceremoniously killed off entirely ended up pissing off quite a lot of people, and they immediately said as much. Not only is the appetite for Destiny still there, but the announcement also furthered the rift between Destiny and Marathon players, with the former now having a good reason to hate the latter's game of choice (remember, Bungo said a while back that they had no intention of stopping Destiny support after Marathon came out). Now you have pretty much the entire Destiny fanbase rooting for Marathon's demise regardless of whether that means more Destiny or not, not to mention the outpouring of support from Bungie devs past and present and the game's voice acting cast. Probably not the best decision, eh, Jason?
Like I said, this is entirely speculation, and Hanlon's Razor may very well be the correct interpretation of events. But it did make me think back on those various decisions over the past decade and how they didn't seem to make sense until I looked at it a different way.