When ESO was released, the scenario provided is that the Imperial Throne was vacant and the three factions, many formed out of little more than necessity and pragmatism, were battling for control of the Imperial seat of power. At the same time, Molag Bal and his forces were dropping Dark Anchors all around Tamriel. I mention the Dark Anchors because they mark a certain chronology point.
So what we have is the Cyrodiil PvP zone where the three factions come together and fight, and the non PvP zones where we take the battle to Molag Bal. Eventually, via the main quest, Molag Bal is defeated... But the battle in Cyrodiil persists. Not surprising since we learn in the Imperial City DLC that Molag Bal, or agents of Molag Bal, are still at work in Tamriel in the Imperial City.
However, in effort to defeat Molag Bal, we see the leaders of the three factions come together, allying in mutual interest to defeat the Daedric Prince of Domination. Craglorn occured somewhere in there but is largely divorced from rest of the story which was happening at the time.
This, to me, marks the beginning of the end of the Three Banners war.
The next major DLC was Orsinium. Orsinium is an Orcish stronghold, but doesn't really consider itself a part of the Covenant. It's got it's own problems, and so doesn't persecute in regards to who is going to help them out. In fact, if they've animosity toward anyone, it's their supposed allies the Bretons. Interesting point of note... No Dark Anchors in Wrothgar. There is one "Unfinished Dolmen" I'm uncertain if it's still under construction, as the cultists present are performing a summoning ritual very different from those typically witnesed at Dark Anchor points. The take away here is, there are no operational Dark Anchors in Wrothgar.
The following thre DLCS also all lack both inter-faction conflict, and the influence of Molag Bal's minions (no Dark Anchors anywhere); Abah's Landing and the Gold Coast both being essentially neutral zones uncontrolled by any faction, and Shadows of the Hist being just a pair of dungeons.
So what we're seeing is a pattern of inter-factional conflict becoming less and less prominent as the influence of Molag Bal wanes across Tamriel, culminating in the release of One Tamriel; the big release that made factions meaningless outside of Cyrodiil. Then Homestead, where members of any faction are now capable of purchasing land and establish residences in areas controlled by opposing factions.
To me, that's sort of the final straw. The war is over when you allow the enemy to reside in your territory.
And that brings us to Morrowind; Chapter Two, the new story. No longer are we (new toons) the reincarnated Vestige, Molag Bal is gone, the world has moved on... And worse, we're beginning to see the fractures in the Ebon Heart Pact. With no great conflict to hold them together, tensions are rising once more among these three cultures with a long, turbulent histories.
What will come of this Chapter? And will future Chapters show us the slow dissolution of other factions?
"But wait!" you say, "People are still fighting in Cyrodiil."
Which is true, so we've got a couple of options here to reconcile this. We can either assume that Cyrodiil, like all the Vanilla zones, exist in a sort of out-of-game temporal stasis that you can return to and experience at any time you want because it's a video game. Or we can go with a more lore-friendly reconcilliation...
Prior to the events of ESO fleshing out the details, the time period we're currently in was sort of this gap where the Imperial Throne sat vacant and various Emperors came and went... Is it possible that the Three Banners War is over in any official capacity, and those people still fighting over Cyrodiil represent the various disparate, nameless, factions seating and unseating Emperors during this ever-so-vague time period in Elder Scrolls lore? That though they still fly to colors of the three factions, none of them truly represent any sort of official agenda?
Either way, to me, the Three Banners War has ended
"As an online discussion of Tamrielic Lore grows longer, the probability of someone blaming a Dragon Break approaches 1." -- Sheds' Law
Have you seen the Twin Lamps?