Secrets are all over Minecraft Dungeons. The game has them ingrained into every level, and if you beat the game once, you need to go through the campaign one more time to unlock a secret level. The secret level can only be accessed if you acquired each rune from the levels. You may have encountered the first one in Creeper Woods, the pressure plate where you save the villagers, but you could not access it because you had not beaten the game. You can find another close to the end of the Obsidian Pinnacle.
You can find the secret when you enter the second area of the level, which is the first interior building you enter. You probably recognize because shortly after you enter this location you have to find a mini-boss, normally it’s a Redstone Golem, but it can also be an Evoker. After you beat the boss, you need to progress through this are of the level until you a larger open space, which looks similar to a library.
Approach the back wall and closer to the left side of the bookshelf will be a book you can push. Push it, and the shelves will push back, revealing the secret room. Head inside and you can find two chests, along with the long-awaited rune to complete your collection if you have already collected the rest.
You can bring the final rune back to the church in your camp to complete the set and move on to the final mission, which is an easter egg to Diablo 2.