There are these mechanical mole-like creatures popping up all over the land (they'd probably need a name).  Ruining crops, causing damage to buildings, and generally annoying people.  They range in size from little, to really big.

They were guardians of an ancient magical civilization, and they have lied dormant for centuries, until now.  No one knows why they are coming out now.  Well, someone does, but more about that later.

What is known, is that the different types have different weaknesses, related to powerful relics that can be found in these ancient ruins.  So, each ruin would have one of these relics, representative of a different type of magic, all with a different function, but all can be used to destroy a different type of the mole things.  Without the item pertaining to the specific type of mole-thing, it can only be temporarily disabled by normal attacks, not permanently destroyed.

So in order to free the land from this menace, you go out in search of these relics.

Once you have gotten a few, though, you catch the attention of this evil dude (he probably would need a name too).  He has unleashed these things to create chaos so he could TAKE OVER THE WORLD!!!  Big fight, he ends up running off though, after nearly finishing you (in one hit) and saying you are puny and no threat.

So you dust yourself off, and get up.  It turns out one of the relics is just what you need to defend yourself from his attacks.  So you're off to get it.  But, oh no!  His minions are in the ruins, and they destroy part of it forcing you to find a different way through.  You do that, you beat the boss, get the relic, and head onward, ready to fight anything that may stand in your way, or so you think.

So you go to get the next relic, maybe a couple minions are around to fight you.  You get to the boss, fight it, defeat it, but wait!  It appears to be taking a new form!  Evil dude's right hand minion pops out and says something like "We upgraded this one, you will never beat it!"  Runs off to let it finish you.  It's beatable, just a little harder.

So then, you go to the last place, to get the last relic, the big powerful one.  You beat the boss, but when the door opens to the room with the relic, EVIL DUDE COMES AND TAKES IT!  "Thanks for clearing the way for me, now I can use this to DESTROY STUFF!"

Noooooooo!  You needed that! :(

One thing to do now, go take it back from his evil lair!

But how will you find his evil lair?  Just look at the horizon, it's that big dark spooky tower over there.  How did you not notice that before?

So you approach its big gloomy scariness.  And go in to beat this guy once and for all!

So you get through his tower, defeat him in a dramatic final boss fight, get you relics together, and use them together to destroy the mole things plaguing the land.

*NEVERMIND*An evil king who is rival to our country has decided to invade and annex our wonderful home of (insert awesome name for a country here). However, the rival king doesn't want to start a massive, land ruining war; instead, he gathers his six court wizards and has them create seven powerful spells, on for each of our country's main cities. These spells will sink the cities deep into the ground, leaving the land clear for invasion and easily taken over by the rival king!

There're seven magical artifacts linked to each guarded within a temple in the rival king's country, guarded by automatons given life by the artifact. When you destroy the artifact within the temple, the city it's linked to pops back up from under the ground and all the life goes out from the temple. One of the wizards also dies when an artifact is destroyed. The final artifact is a necklace or ring or staff of some sort which belongs to the rival king, and you have to destroy it and kill him, etc, etc. 

You escaped being buried with all the people because you were part of an escort to a diplomat who was going to the rival king's country to try to create a treaty, and you hear chanting while you are in a hallway and go to check it out. You see the wizards and the king all circled around a gigantic, magic-focusing device which is at the center of the castle. They sink the cities, and you keep watching until the entrance to the first temple is mentioned and you go to it.

At the end, when you finish facing down the rival king and destroy his artifact, you get a surprise! The rival king was just a steam-powered automaton who had been stealing the REAL king's magic and authority for years! There's a flash showing how you killed the real king who's locked up in some tower, and then the automaton king attacks you again and you have to kill it before you return to your king and are happy, get rewards, and the like.

The minions within the temple are often floor based and pop up. The type of minions depends on what the theme of the temple is, but most of the start in the ground before popping and trying their best to kill you.

Or, alternatively, you could have to collect the artifacts and combine them with the big magic focusing device after destroying the rival king to create a reverse effect and save all the cities at once.*NEVERMIND*

Evil Bad Guy is building cities beneath the ground, filled with his evil minions! They keep popping up from beneath the earth, spreading their malevolent influence to all around them and destroying the countryside! OH DAMN! So, our hero goes beneath the cities in an effort to destroy their supports and sink them back into the bowels of creation where they BELONG. Too bad the supports are guarded. That's where Hero's weapons come in. To destroy the supports, Hero uses steampunky burrowing devices and the like. All the cities are buried again. Yay! Evil Bad Guy is gone for good!