Fate/Zero/WMG

The massive fire/death/destruction was not Kirei's wish; it was Gilgamesh's.
Earlier in the novel, Gilgamesh informs Kirei that he should get a wish ready even if he doesn't have one because the Grail grants whatever wish is closest when it manifests; usually that's the winner of the tournament, but it doesn't have to be.

Kiritsugu shot Kirei after their fight, and since the 'mud' of the corrupted Grail had to build him a new heart to get him on his feet we can assume that he was functionally if temporarily dead. With Kotomine dead, Kiritsugu having rejected the Grail, and Saber's failure to get her wish a Foregone Conclusion, the only being left around - and who was actually inside the Grail, not to mention managing to metaphysically overcome it and escape - was Gilgamesh. Though his later wish is to rule over the remnants of humanity, his over-arching interest throughout Fate/Zero is alleviating his boredom; by the halfway point he's clearly settled on Kirei as the most likely prospect to achieve that goal.

Having prodded him in the direction of The Unfettered over the past several chapters, Gilgamesh knows that all Kirei needs is some kind of validation to prove his 'inversed soul' should be satisfied: Conjuring a scene of such devastation, which he knows will appeal to Kirei's 'joy,' is more than enough to get the priest to accept his distortion and proceed along such a path. Which of course, for Gilgamesh, is Just As Planned: Now he has someone to keep him supplied with prana and entertainment until the next Grail War comes along and makes him King.

The long-haired man (or the cowled one) seen inside Ionioi Hetairoi in episode 11 is the future Waver.
Let's think it like this: Ionioi Hetairoi is, in Iskander's own words, generated by the feelings treasured by him and his warriors; so strong those bonds are, that the power of the bond coalesced and formed a Reality Marble. Now, we have little proof if present!Waver will indeed go on and die a Heroic Spirit, but Iskander and Waver have undoubtedly forged a treasured bond between them. By that merit alone, I think Waver had more than earned his place to walk beside Iskander in Ionioi Hetairoi.

Also, the Throne of Heroes is situated outside the passage of time. Even future heroes (EMIYA) can be summoned from it, as FSN!Rin has demonstrated. Now if Ionioi Hetairoi somehow summoned the spirits bonded with Iskey from the Throne of Heroes, it surely can summon future!Waver too.
 * It even says as much in the novel--that Waver and Rider's bond is beyond time, that is. To quote: "There was no need for words. From this day until the end of time, the servant would be guided by the figure of the King, and the servant would remain loyal to that memory. In the face of the oath, even separation was meaningless; under the command of Alexander, the bond formed between King and servant was eternal and beyond time."
 * It doesn't specifically mention Ionian Hetairoi, but it certainly suggests that Rider and Waver are eternally connected to one another, well beyond death. Anyway, as to the idea that Waver can't join Ionian Hetairoi because it's implausible that he could become a Heroic Spirit, this troper thinks that the bulk of Alexander's army is made up of spirits on the level of lower-class Servants, not necessarily Heroic Spirits in and of themselves--unless we're really expected to believe that every single one of that huge body of soldiers that doesn't have a unique character design are remembered and venerated in legend. Alexander remembers them and honors their bond, and they are loyal to him, and that's what counts, not whether or not the world remembers all of their names. In that light, the only possible reason left that Waver would not become part of Ionian Hetairoi is that he and Alexander shared a different dream than that vast desert--but that just leaves open a window for Waver to become a lesser Servant Alexander can call to his side individually, and somehow this troper doesn't think that's an alternative anyone is going to mind.
 * Because Alexander is a Caster now, and thus capable of summoning Heroic Spirits, even lesser ones, who are not related to his actual legend. There's also the point that was made about Alexander being able to remember every one of their names, and the fact that only Alexander's copy met Waver: The original, the real Alexander who knew his army while he and they lived, did not meet Waver, and when that copy died and was deleted his experiences/memories were not transferred to the original within the Throne of Heroes. It's mentioned that even if Waver summoned Alexander into the Fifth Holy Grail War the new Rider wouldn't remember anything that had happened because each Servant is a copy that's deleted upon completion a given War, save for those with explicitly-stated exceptions: Archer EMIYA is a Counter-Guardian, Saber Arturia isn't actually dead so there are no copies of her, only the actual original Arturia being summoned, and Gilgamesh got a physical body and hung around between the Fourth and Fifth Wars so the deletion didn't apply. Alexander, as far as we know, lived and died and became a standard Heroic Spirit, so the rules as laid out would apply. There is such a thing as metaphor, and the way that Waver changes after his experiences with Alexander - even to taking up Alexander's colors - is just as likely if not more so to be what's meant by 'Alexander's figure guiding Waver.' In such a case, mentioning that it's beyond time and space simply illustrates that despite the circumstances surrounding the relationship, including Waver being the only one left who remembered it, Waver still retains his feelings about it as well as the lessons he learned.
 * Out of curiosity, where exactly is it stated that a newly-summoned Alexander wouldn't remember Waver? I don't recall coming across that anywhere, whereas I have come across statements like these, from the wikia: "It is possible for this main body to become aware to some extent of what happened by accessing the records of Akasha." "As is it known that Servants are eventually returned to the Throne after being defeated, it is possible that the summoned Heroic Spirits are able to retain the memories of when they were Servants."
 * In addition, the LN hints that Gilgamesh is an example of one-he's stated to be aware of other times he's beens summoned (no idea who by or what for, likely Alaya or something)to the world, 'to farces that were battles in name only' or words to that effect. In addition, the Throne of Heroes is outside time, so I wouldn't be surprised if guys from the future made it into Ionioi Hetairoi, especially since there's what looks like Roman armour in there-Rome rose after Alexander, and many of its generals were inspired by him. In the end, who's to say?
 * Firstly, I wouldn't recommend taking the wikia at face-value; among other things, it calls Rider's mode of dress "romanian" when it should be Roman and is often uncited. That said, and I'm avoiding a quote-war here, it's made plain in the Fate/Stay Visual Novel (talking about Saber's unique condition as a Heroic Spirit/Servant), the Fate/Zero novel (particularly Kirei's comment about Tokiomi not caring about sacrificing Gilgamesh since he's only a copy), and the supplementary materials (primarily artbooks and interviews) translated as part of the now-defunct Fuyuki wiki that unless it's made plain within a given installment that a particular Servant is "special" all Servants are deleted after a war since they're just copies of a Heroic Spirit. The Throne of Heroes has been established as something like an archive, "saving" those it considers "heroic" in their peak form; the reason copies are created and summoned rather than the real thing is that the Throne considers the spirits in its database to be perfect, so it removes that particular soul from the 'wheel of fate' to preserve its perfection. Changing that data - including adding new data, i.e. memories of Waver - would alter the original spirit's save-state so that it would no longer be the perfect spirit the Throne chose, and thus it would be erased. While it is theoretically possible for a Heroic Spirit within the Throne to access its database, they would likely face the above fate - deletion - unless they're already specified to be exempt from the standard rules. EMIYA, Arturia, and Gilgamesh are three who, as explained, are exempt due to special status or circumstances: Alexander was summoned normally (as a copy) and dispersed normally, so the Rider we and Waver knew during the Fourth War was deleted in order to preserve the Real Alexander saved within the Throne of Heroes. Regarding the above quotes, it would be more accurate to say that the data gathered by the copies, their experiences and memories, do return to the Throne because the Throne is effectively omniscient, at the same time that the power sustaining the Servant in question is dissipated and returns to the Grail/Throne: However, that does not automatically give the original Spirit the memories of their copies, and the Spirits themselves are in a kind of stasis as part of being 'frozen'/preserved in their perfect state so the chances of a Heroic Spirit rummaging through the Throne's database is unlikely, again unless they're stated to be an exception.
 * Personnally, I'd like to believe that this is indeed waver. Alexander is a man who managed to screw the rules of time and space by being simply too awesome for the world to handle. It wouldn't really be weird for him to do it once again to remember waver and welcome him in his personnal guard.
 * There's definitely no reason one couldn't believe it was Waver, and this is Wild Mass Guessing: Combine it with No Such Thing As Notability and MST3K Mantra and you're good. But in the sense of "Alexander less 'screwed the rules' and more 'put up a really good fight while supported by all three Command Seals,'" there's a distinct divide between what we're given in the actual series vs. what would allow such a theory to be true. Again, that's absolutely no reason not to believe it; there's just evidence to say that yes, it would be really weird, Broskander or not.