The League of Legends MMO will have to incorporate the existing League of Legends champions into the game. How they will do it though, is still being discussed.
It's one of the two Projects Riot Games are currently working on, and will be based on the current League of Legends lore. That is,it will be placed in the world of Runeterra, and will set in stone League of Legends lore once and for all.
Greg Street, EP of the Riot MMO project was just recently asked on Twitter whether champions are going to be added into the game as some form of dungeon boss or other creature we can fight:
"We want to treat the champions with a lot of respect. I’m not saying you will never fight any of them, but we aren’t just going to turn to them anytime we are short on boss ideas."
So, it seems unlikely that League of Legends champions will just be the end-game goal of the LoL MMO. However, with champions whose lore is centered around being end-game bosses, it would also make no sense not to incorporate them as such.
The prime example is Kog'Maw, who can be something like a World Boss, in his quest to consume everything. Others, such as LeBlanc can be quest givers. The possibilities are endless.
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