In DROD: The Second Sky, a puzzle video game, the protagonist travels far underground and discovers an entire world beneath the surface. The inhabitants there are strange are often actively hostile. Soon, the protagonist discovers that they're planning to take over the aboveground world, and it's up to him to stop them and somehow get back to the surface.
In Digger, a webcomic, the protagonist travels far underground and discovers an entire world beneath the surface. The inhabitants there are strange are often actively hostile. It's up to her to stop them and somehow get back to the surface.
In Tunnels/Deeper/Freefall, a series of books, the protagonist travels far underground and discovers an entire world beneath the surface. The inhabitants there are strange are often actively hostile. Soon, the protagonist discovers that they're planning to take over the aboveground world, and it's up to him to stop them and somehow get back to the surface.
In Subterranean Animism, a danmaku video game, the protagonist travels far underground and discovers an entire world beneath the surface. The inhabitants there are strange are often actively hostile. Soon, the protagonist discovers that they're planning to take over the aboveground world, and it's up to her to stop them and somehow get back to the surface.
Any others, folks?