Obviously people suggest a lot of things for boss mobs, but this is one that fits the setting, I think.
End - Ender Dragon
Nether - Wither
Overworld - Tarrasque!
A Tarrasque is a horrifying D&D monster of legend. Everyone fears the mountain that gets up and walks away. This is that very fear, come to life!
The way I see it, maybe they only spawn in Mountain biomes, and extremely rarely. You can mine into it, without waking it up, as they are creatures who hibernate for hundreds of years, so it's hard outside is in part actual Earth.
Waking it up, I've got a couple ideas. Hit an organ, maybe? Maybe it's more of a Golem in Minecraft, and the mountain it is has a temple within it that you have to build and place a key of sorts to wake it up, which exposes it's weak spot(s).
Then how you fight it. It spawns creatures that try to defend it, akin to an immune system, and if you die, you'll return to your bed, and it will continue to roam until you can re-board it. It's not outwardly aggressive, but is extremely dangerous to be beneath, and to get back on/in it, you have to build up. Anything you built on it would break as soon as it woke up.
Just spitballing some ideas. Thanks for taking the time to read.