Riot, Here's a better way for you to get rid of the IOW: Have it be DESTROYED by a new faction
Lots of people are pissed that you are simply retconning out the Institute of War from League's lore. That's way too lazy, Riot. You want to do it right? Introduce a new faction, and make it so that this new faction DESTROYS the Institute as its first demonstration of power.
The faction I'd choose? DRAGONS.
League could definitely use a Dragon faction, one that is pretty much an enemy to all of the other nations/factions, but is so powerful that they can't take them on recklessly.
Here's how I'd write it, starring one of my old Champion Concepts (fairly rough):
Many millennia ago, Runeterra was ruled by the Dragons, who had enslaved the other races under them to bring order to the world and safeguard it. The Dragons were ruled by a cruel black dragon known as Plagueis, who crowned himself the Dragon King after leading his brethren to subjugate the mortal races.
Plagueis ruled for one thousand years before a human uprising occurred, led by a warrior who commanded the power of the Sun (yep, Leona's ancestor). After a series of victories against the Dragons, this warrior challenged Plagueis to single combat. Overconfident, Plagueis accepted the challenge, and was slain in battle.
Following Plagueis' death, the Dragons dissolved into infighting over scraps of territory, leading to ultimately fatal battles between the Dragons, who were also hunted by their former slaves. In time, memory of the Dragon Age was lost, except to a few elder Dragons who have survived since such ancient times.
Now we return to the modern age, where the Institute of War exists. A group of Summoners, ordered by the High Council of the Institute, make their way to Plagueis' old lair, a high mountain named Death's Spire. They find Plagueis' bones in the lair and perform a magic ritual to resurrect the dragon and turn it into a mindless thrall. However, they did not count on Plagueis' dark spirit lingering within his bones, and as he was given new life as a Dracolich, he "rewarded" the Summoners with a swift death. Learning of Plagueis' return, the High Council sent a contingent of Adjudicators to kill him, but Plagueis escaped.
Learning that the Institute of War wished to control the remaining Dragons in Valoran to give itself an army (in order to police the other factions), Plagueis was infuriated. He rallied together many other dragons, some who had been his loyal lieutenants during the Dragon Age, and formed a small but powerful army. Plagueis and his followers attacked the Institute of War, completely overwhelming the Summoners and Adjudicators, killing the High Councilors, and burning the Institute to the ground.
Within the ruins of the Institute of War, Plagueis created a new lair for himself and his subjects, and now he seeks to reconquer all of Valoran, and return Runeterra to the days of the Dragon Age.
See, Riot? This could be MUCH better.