Whether you are writing a novel or a short story it is best to have your MAIN PLOT before you get too much written down.  The Main Plot is the singular thread that runs through the novel/story.  You may have character ideas or scene ideas but eventually you need to think about a plot.  Do this sooner rather than later.

The best way to do this is to list your main characters and then decide what are their individual main plots. Are they all on the same quest with the same ideas / goals or do some of them have their own goals?

To help show this, here's an example:

Main Characters
Eric – To become knighted and serve his king
Vivian – To destroy her former master before he can poison the kingdom
Luke – To find his brother
Taldor – The largest city

Maybe from this list you decide Vivian is the MAIN character and her story line is the driving force however each of the other three have story lines that need to be told.  The main story is where all the threads come together.

Vivian's former master Rayn has travelled to Taldor where he will poison the Royal family and the nobles, with these higher powers gone, the peasants will be easier to control and he can rule.  Vivian is following him, but the master knows this and has her arrested in one of the towns.

Eric is travelling to Taldor where the five year tournament is being held for new bloods to show themselves and possibly become knights.  (here we are tying him in to the main story by having his destination the same as Vivian's)

Luke's twin brother Torris is missing, Torris joined a clan of thieves and has not been heard from again.  Luke is visiting local towns where he has heard sightings of his brother.  During one of his visits he gets arrested by mistake as the local guards think he is his brother.  (here he meets Vivian in the gaol).

From this example we have three main characters each with their own plot but we have decided that Vivian's is the main.


THE SKELETON
The above is your story skeleton, the bare bones of an idea that gives it form and structure.  To get it solidified your need to write the plot in bullet points.  Keep it basic and remember this is just the simple threads.

It can help to do each character plot at a time (especially if there are parts were the characters are not together)

For example:
Vivian Plot
* Learns of her master's plan
* Escapes from the manor where she was imprisoned by the master
* Follows the master through several towns
* Master Rayn finds out she is following and plots her arrest
* Vivian is arrested
* Vivian meets Luke
* Luke and Vivian escape and are chased by guards
* Vivian and Luke are rescued by Eric
* The three continue travelling to Taldor, during this time Luke learns more about his brother's whereabouts
* Master Rayn learns of the trio and makes more attempts to stop them
* They arrive at Taldor and Eric goes to the tournament, if knighted he will have an ear to the king and be able warn him successfully about Rayn etc.


As you can see from the above, you will eventually have a basic list of plot points listed.  If you did this for each of the main characters you can then begin to intermix them all.  So you end up with a full list of bullet points.


THE MEAT
Now you have your bullet points of the basic story, you can start to write it but be aware that this still needs "fleshing out".  The meat of your story is as you build on it.  The best way to do this is to ask yourself questions.  These questions will allow you to add new dimensions to your story.

Example:
* How did Vivian become a slave to Rayn?
* Who is Rayn and why does he want to rule the kingdom?
* Why did Luke's brother leave?
* Is there a bigger motivation for Eric wanting to be a knight?

These are possible questions you can pull from the above examples.  If I answered these (see below), you will see I could develop the story on a deeper level.

* Vivian is sold to slavery by her mother who needed the money to raise her other 6 children.  Vivian took the burden from her mother and volunteered so her sisters would not have to suffer the same fate.

* Rayn was born to the late king out of wedlock, his mother is a lower noblewoman.  He sees himself as a true heir because the king's son to the queen (who is now king) is younger than him.  

* Luke's brother left home due to the debts he had accrued to a shady man.  He feared they would attack his family to force his hand so he fled so that they could not use his family against him.  (Did they anyway?)

* Eric wants to be a knight because his abusive father always told him how worthless he was.  The highest role a commoner can achieve in society is as a knight.  Knighthoods are only usually offered to men of noble birth, however in the first year of a new king everyone of skill is given the chance to show themselves worthy.  This is Eric's only chance to prove himself.   

It is by planning the basis of a plot and then asking yourself questions that can help you build on a novel/story.  

As you do this, more questions may become apparent.  It is from these that you can turn a basic plot into a multilayered, multiplotted book.