Were the Shadow Isles existing long before the Rune Wars, during or after?

I am writing a Fan Fiction Lore that aims to be as accurate as possible to the Lore Universe. Here are some notes I have taken:

The Altar "spirits" were husband and wife
They lived a thousand years ago
The king is mention by the Altars as the King of the Isle
"Spider God" inhabiting the Island
Large population of undead

Help will be much appreciated!

0.=

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Okay, I've had thoughts on his matter, but they excluded some of tour points. Still, I'm going to try and take everything you cited above and combine it with my ideas:

So we start off 1000ish years ago, with the husband and wife rulers (the two spirits of the altars) of an island kingdom/province (what would become the Shadow Isles). It's all good, but then Mordekaiser - a human of some kind at this point - begins a rebellion to control of the island himself. Battle rages, and awakens a number of evil creatures (the Spider God) but with his considerable power Mordekaiser finally wins through and kills the rulers.

Mordekaiser is a powerful necromancer, his entire army being made of the soul and corpses of his fallen enemies, and in order to continue to bind their powers to his service (the rulers of the island are powerful in their own right) he seals the souls of the husband and wife in a pair of altars. However, as said, the rulers of the island were powerful magi a well; and with their last bits of free will bind Mordekaiser within his armor; limiting his power. Even with this, though, Morde's power is still mighty enough to let him maintain his minions, call more when need be, and rule over the island (keeping things like the Spider God at bay).

Hecarim, a Centaur warlord of another land, dies in battle sometime later and, due to the now-reeking power of the necromantic magics hazing the island his soul is drawn there. Morde makes a deal with Hec, Hec himself has developed (or maybe always had) considerable magic post-death (similar to how Yorick is suddenly able to call ghouls, despite being just a gravedigger in life) and he and Morde agree that they will combine their powers and forces (Hecarim's undead centaur/mounted warrior army, visible in his ultimate) in order to conqure the world, both being very power-hungry and war-mongering.

However, first Mordekasier needs to be free of his armor to reach his full power, and Hecarim will help him with this; what Hec does not know is that the moment Morde is free, he will have enough power to ensalve the Shadow of War (based on the altar's warning to Hecarim). Yorick also reaches the Shadow Isles around some point, and makes a deal with the two (or one or the other) that they will help him reach his true afterlife if he assist them (by making more dead for their armies, based on the altar's command).

So, in short; Mordekaiser rules the island, Hecarim and him have a plot to rule the world, Morde intends to backstab the centaur the moment he is free of his binds, and Yorick is a poor soul indebted to greater masters.

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This next part is unrelated to the above, but was just speculation on Elise that crosses my mind:

Elise then comes to the isle, and is taken in by it and the Spider God/demigod (who knows that Morde will enslave him as well, should he get the chance) as a means of protection. However, Elise is too cunning and, upon the creation of the Twisted Treeline in the Isles (known to the champions and a few civilians, but most don't want to believe (who would want to believe that there is an island filled with the living dead?)) she is able to harvest his venom for her immortality and power; so she no longer needs her cult (to travel to the Isles and sacrifice to the Spider God for venom) and she no longer needs her human guise (which is why she does not mind flaunting her true form in the League).

I've always thought of Morde and Hec as equals, both representing two of the riders of the apocalypse, with Eve, Karthus, Elise and Yorick hapless mortals that have been to some degree drafted for their cause

Morde and Hec aren't directly affiliated with each other, as it has been stated that they have a disagreement on how to reach a goal they share

Karthus and Elise are both power hungry mortals who went to the isle for power, and found it

Yorick's existence suggest there is, or was, a habitable part of the isle

They are equals, but because Morde seems be looking for something (in my mind, a way to escape his prison/inhance his power) it's clear he has something of the advantage, or may gain it.

And if you listen to the the altars in Twisted Treeline, sometimes the female one will say (when capturing a point with Hecarim) "Do not trust Mordekaiser, Hecarim). This suggests something of an alliance between the two.

I don't recall Karthus every traveling to the Isles; he found his own way to power on the mainland. But it seems the lore was changed; so you are very much correct.

Or the part of whatver habitable land housed Yorick's cemetary collapsed into the ocean as the world's tectonic plates moved and shifted. I didn't think to look back to see if Yorick couldn't find his cemetary before or after leaving the Isles

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The goal Hecarim and Morde share are to take over the world aren't they?
And Elise isn't power hungry. She just worships a spider god.

Karthus isn't power hungry, he just has an obsession with death. He wanted to embrace death because in death, life gains meaning. He didn't even want the power given to him by the Shadow Isles, he simply wanted to feel at home, at peace. The power given to him is simply because he willingly gave his life to the Shadow Isles, and the Shadow Isles returned his trade with power.

I sort of want to see a live version of them now. I figured Hec would just be your average horseman.
Anyway, I believe the closest thing to a goal that Hec and Morde have is the showing the power of the Shadow Isles. Yorick is the guy who can actually get them the dead soldiers. Eve is currently unknown but I guess she's fairly alive so I can assume that she's one who managed to get away not dead. Karthus and Eve were just people who needed power.