Now, to me, the signs of the prophecy about Alduin's return dont make a lot of sense (since when divinity made sense anyway?). There is however, a piece of information that sort of holds it together, but its a biased piece of information from Camoran (from Oblivion), and him being a Daedra worshipper, maybe relying on him isnt the safest bet.
Acording to Mankar Camoran Lorkhan is actually a Daedra Prince, who had been tricked out of his daedric plane (Nirn, the "real" world). Now, he mentions something else, that I dont remember accurately, but can be constructed as Lorkhan being tricked by the Divines, leading to the whole thing about his Heart, ect. However, Camoran seems to imply that the Covenant with Akatosh was part of this trick, where the rest of Oblivion is sealed from Nirn, and the Divines seem to have free reign on this usurped daedric plane that Nirn is.
So, if we take the events of the Prophecy as tied to Lorkhan, they start making sense. It is believed by some that Tiber Septim has the same essence, via an Oversoul, as the Underking and that other guy from Daggerfall (forgot his name). The three form the figure that is known as Tiber Septim. However, it seems there's a belief (which I read in the Elder Scrolls Wiki, but it doesn't have a reference, as almost nothing in that wiki), that this Oversoul was somehow administered by Shezzar, which is just a Cyridiilic interpretation of Lorkhan. Thus, by the deeds of the figure of Tiber Septim, Shezzar, known as "the Missing God" of the Eight Divines, ascends to be venerated as a divine (Talos, therefore now being Nine Divines). So, in some sense, it is Lorkhan plotting to become once again a part of the world he designed (or, as Camoran would put it, a plan to retake his daedric plane, stolen by the Divines).
Taking all this into account, the events of the Prophecy seem to hold together. I have found no info as to where the Staff of Chaos came from, but since Arena says it was created "from the Land itself", we can assume there's some essence of Lorkhan there, since part of his essence fell to Nirn after his body split (the Moons); also there seems to be some connection in the Staff's abilities, which basically gave you free passage to Oblivion (which fits into the conception of Lorkhan wantin to return to his world via some means). The return of Numidium also might tell us something, since it was to be activated by the Mantella, which mimicked Lorkhan's Heart, and I THINK it had some essence of Tiber Septim or something (which would be interesting if we hold to the Tiber Septim/Lorkhan Oversoul theory).
Now, the events at Red Mountain need no explanation, since Lorkhan's Heart was part of the plot. The Oblivion Crisis seems to have shaken things, allowing Daedra to roam freely in Nirn.
In the end, this is what I think: All of this establishes in my mind the possibility that the events of the Prophecy are tied to a plot by Lorkhan to regain what was his. This is taking as true the Camoran theory, however, its the only thing that for me can make sense of the prophetic signs. Now that the Dragonfires are forever dim, and the Dragonborn line that could use the Amulet of Kings from the Covenant with Akatosh no longer keep these fires lit, Akatosh's designs are in ruin. Therefore, the return of Alduin, the second aspect of Akatosh, as the destroyer, which would be a natural opposite pole to Time (Time-End Time, Beginning - End).
I think the return of Alduin heralds the destruction of the world by the Divines, since they can no longer keep hold of it by keeping the essence of Lorkhan (or any Daedra) at bay.