Ok, obscure misleading intro out of the way, I'll start writing well again. The most important aspect of any plot is a concrete, structured theme. Let me repeat that: a concrete, structured theme. What this means is you set a timeperiod, a place, a mood, and you develop the entire plot around that. Perhaps some examples will help. If you've ever played the Ultima series, you will notice that the original theme was based upon the British Midieval period in the height of feudalism. By Ultima 4, the theme followed history and developed into a large medieval country, similar to the chronicals of King Arthur. Everything follows from that!!! You have your set of heroes and heroines (like the Knights of the Round), you have your medieval weapons, armor, and transportation. You fight dozens of mythical creatures like dragons, hydras, orcs, etc. And you follow a main quest from Lord British (parallel for King Arthur) which may divide itself into several subquests along the way which you are obligated to play because your character follows the Virtues of the land. In other words you must complete these quests just like a Knight of the Round would in order to follow the Code of Chivalry. Following this? The parallels are rather blatant, but the series is making its 9th game now! It's that good, it has that concrete, structured theme that makes the world so realistic and the game so much fun.
Now, that is a game series that is probably older than most of you (Ultima I was originally on an apple way back in 1979), so don't think you have to make a series as great as Ultima. Rather, just take the concepts it presents to make a good game. It doesn't have to be medieval; many futuristic and space RPGs exist. Also Square's Final Fantasy series has moved over the years to encompass a technologically advanced era with a midieval feel. The original was purely midieval, Final Fantasy III (US release), was medieval with technology mixed in, and by VII the medieval aspects were almost non-existant. They were able to do it by developing a concrete theme of an evolving world in which each game is only a chapter in the whole story, never putting too much evolution in at one time.
Ok, I've filled you with all sorts of ideas - now what to do with them. Well, let's take just a standard pirate theme. This means that no matter how much you want there to be a nuclear sub that you use to blow ships out of the water, you can't put it in the game. You must also remember that you've now confined yourself to a post renaissance era - no mythical beasts, no magic. Your technology is swords, cannons, and muskets. Your boats are small, 15 man ships, to huge 200 man galleons. You're probably thinking: what fun is the story now? Well, remember that there will be people who won't want to play a pirate theme, but there are more who would if you do it right!
What makes piracy so much fun? The adventure, the thievery, raiding, cannons, secret romances, corrupt provincial governors, and of course, yelling "AAARRRR!" You have your wonderful theme right in front of you, now use your imagination!!! Think of one great, all-encompassing purpose for your game. How about destroying the corrupt armada of the bad guy? Here's where your background information comes in. There is a corrupt official who using his military prowress in the water has subdued and captured 75% of the coastal towns in the game and is using this to control all the trading in the seas. As one of the citizens of the few remaining free towns, the only way you can survive in your trade is through piracy - sinking the bad guy's ships, raiding his towns, sailing in his waters, etc. Your ultimate goal would be to kill this individual and free all the towns under his command. Ahh, but how can one small man do such a thing? You obviously need to go on several subquests building your own group of followers, wealth, and armada.
If your following this, we've now tackled two things: a concrete, structured theme and a main quest. Now comes the easy part, the subquests. Remember that they also must follow the theme. Let's start with an easy one. If you've read up on piracy, many pirates were English noblemen. Since your character is a good one, from a free town, you could make him a nobleman and perfect gentleman. That way, winning the heart of some important woman in one of captured towns wouldn't be a problem. After sinking or stealing 12 ships from the bad guy, you return to a free city for repairs where a mysterious note had been deliverd while you were at sea. It is from the daughter of one of the governors in a captured town. She has been betrothed to a local captain, an evil and disgusting man. Having heard of your great valor and deeds in helping free the towns, she has determined you to be her savior, someone who could steal her away from her troubles. Naturally, you now go out to sneak into the town under the cover of darkness, kill the guards in her mansion and sneak out under a full moon with her. Yes, I know it sounds a bit cheezy, but think of your theme! It fits right in and people who play it will know it. You could add many, many more subquests, like gathering the pieces of a treasure map, freeing local towns, raiding a galleon at port, sinking the ship of a rival pirate, capturing a government official and holding him for ransom, etc. Just don't add any sea serpents or jet bombers...
That about covers it, you should be set. Remember your theme could be something as ridiculous as space invaders. Just remember to develop your game around little green men with lazer guns. The quests should follow the theme and they don't have to be elaborate, just as long as they fit within the world you have created. Good luck!