Think of the basic conflict and basic resolution first. It's kind of like making a sandwich. You know there's going to be two pieces of bread, so you know you can start there. Think of whatever conflict motivates the story to take place (like aliens invade the Earth) and then how you want it to end (all the aliens die and Earth lives happily ever after).
Come up with any basic heroes or villains. Maybe your hero is an entire village or a feisty princess. The villain could be an evil king or a virus. Either way, good story lines almost always have a good guy and a bad guy involved, be it people or entities.
You should also flesh out the main characters with their good and bad qualities. Sometimes the most believable villains are ones that have similar positive qualities and goals but have chosen the least popular paths. For example, The "X-Men"'s main foe, Magneto, wanted the same thing Xavier wanted: respect for mutants. But Magneto felt humans weren't worth saving. Heroes with believable faults make it easier for audiences to relate in the same fashion.
Take the faults and qualities and use them to create plot twists. Superman's weakness was Kryptonite. Many good stories about how Lex Luthor could expose Superman to Kryptonite were made. Lex Luthor's faults of greed and revenge always blindsided him from successfully capturing Superman.
Decide on a tone for your story line. Will this be a serious story with morals or lessons emphasized, or a comedic take on a normal issue? A wronged man falsely imprisoned can be as serious as "The Count of Monte Cristo" or as funny as "Ernest Goes to Jail." If you are very creative, it can be both serious and funny.
Add supporting characters and a setting. Supporting characters have a way of enhancing the heroes' and villians' motivations and characteristics. They sometimes have a way of changing the story or twisting the plot, like Rosencrantz and Guildenstern in Hamlet. A setting can add a mood to your story line. Setting it in L.A. can give an air of a fast-paced lifestyle, while the countryside of Wyoming can add warmth. Settings can also affect characters and their interactions. Two people fighting is one thing; two people fighting in the middle of a Montana blizzard may change their plans.
Draw a linear picture of the beginning and middle of the story line and make notes of where the plot changes or thickens. Write out descriptions of characters like "good-hearted cop" and "rich megalomaniac." These descriptions should be five words or less. Note the setting. Place the notes next to your word processor as you type out the story.