When I get ready to run a new campaign, I have to make sure most of my bases are covered. First, I start with the world. This is not so difficult with Palladium games where most of the world is planned out for you. But for arguments sake, lets say I am running in Phase World/Three Galaxies setting. I would make the world/worlds that I am going to be using (even down to minute details such as imports/exports, how many troops/ships they have, system of government, etc.). Each of these worlds would come with major NPC's, maps, special OCC's, maps, solar system data and yet more maps.
Second, I decide on the flavor of the story. Is it going to be Horror? Militaristic? Intrigue? Treasure Hunt? Free Range? This is going to determine how I lay out the story and what kind of timing I will be using for the scenes.
Third, I start on the story. I conceive the reason that all of the characters have been brought together (if they don't know each other already through back story). Once that is accomplished, I move on to their first plot hook, something to get them involved in the story. From there, I develop other "missions/stories". This is usually done separately so that I can organize them later in a timeline style progression ( a maturing of the story if you will) that make a bit of sense. Once I have a few of these "missions", I find a way to weave them all together in an overall metaplot if I don't have one already.
Fourth, I design any items (tech, magical or otherwise) that I need for the forseeable future. I then insert them into the story taking shape in a Word document as sidebars, text boxes, pictures or whatever. Sometimes I link the reference to other documents (mostly for stat block purposes).
Fifth, I make a separate file to keep notes on the game as it unfolds. This is used to make any needed adjustments to the metaplot as it unfolds. This is because most plans never survive first contact with players.

Lastly, I just keep working away on the story as the game unfolds. After each playing session, I polish the parts of the story that have yet to be played and makes notes on what would get changed if it was ever run again.