The first step is the start and the end. (deviantart)
Decide how you'd like your story to start and end before you start writing it. You can figure out the middle as you're writing it. If you don't know how it's gonna end when you start it, you run the risk of writing a plotless ship story.
For the ending, it doesn't necessarily need to be a detailed one. Even an outline like the MC having a family on a quiet farm is enough. But you need to have it in mind, most definitely.
The second step is figuring it where to put the main events in the timeline.
Let's use Marvel as an example. When the chitauri are going to attack? And Thanos? Galactus? Is this gonna be near the beginning or the final of the story?
Make a rough outline to at least more or less know if the events that are to come are closer or distant than others. Just having this already organizes the timeline and frees space in your mind to think about other things in more detail.
The third step is the middle of your story.
Remember the notes I said to you to keep writing in the [Mindset] chapter as your mind and unconscious come up with random ideas? That's one of the few reliable methods for coming up with at least some side plots to put between important events and even major events like totally original ones.
(Through the course of the story make past facts, events, decisions, etc, have consequences and be connected to the future, remembering past events in future chapters. Each action has a reaction.)
The fourth step is trying to stick to the canon. (DeviantArt)
Before anyone jumps in with an "OMG it's fanFICTION, I can do whatever I want." I know that you can write whatever you want; I'm just trying to be helpful.
Let's go back to marvel. If you denied the chitauri invasion, the Thanos invasion, etc, you are more than likely to lose readers and miss major plots unnecessarily. Besides, I think we can all agree that if you turned Sasuke from Naruto into a chicken farmer, you might piss off many people, and their reaction is completely understandable. Be reasonable with your fanon material.
As time go by, should you follow these steps, your timeline of events will gradually get fuller and sharper. Trust me on this. Source: Me :oD
Also, be original. (DeviantArt)
It's easy to fall into overused plots (i.e. _____ is in love with ___, but is too afraid to say, will they end up together?). Read some other fanfictions, if you find any plots that you think are used too much, don't use them. You could also go on Forums to see what plots others think are overused. More people will wanna read your fic if it's about something they're never read before, instead of something they've seen a million times. And no matter what, DO NOT STEAL THE WORK OF OTHERS. They worked hard on it, and not for you to take credit.
Another thing to note is things to be careful when planning and how to avoid "plot fatigue", as said in tvtropes.
Perhaps the biggest pitfall in fanfics at the moment is the lack of planning. Many fanfics are conceived from inspiration for a central plot twist or a really good ending. Unfortunately, the audience will never see that twist or that ending because the author never considered how they would get there, and doing so becomes a long, tedious, boring journey for both the reader and the author, resulting in the author losing interest and the fic becoming dead. To prevent "plot fatigue" from happening, try one of these things:
Try a smaller scope. Your fanfic doesn't have to be an epic 100-chapter saga. Try a one-shot or an 8-chapter piece first, and see where that gets you. You may learn something about yourself.
Or, if you're dead sure you want to make that 100-chapter saga, try making the whole thing awesome! Don't wait until Chapter 86 where Alice finds out that Bob is her brother and that they're actually stuck in an alternate dimension... Instead, why not plant a juicy plot twist or new revelation in every chapter? It'll keep you interested and it'll keep the audience dying to know what happens next.
But keep in mind, there can be too much of a good thing. If it ever feels like you have to get your revelations from out of your lower intestine somewhere then give yourself a Breather Episode or three. Trying to steadily increase the awesomeness all the time can add more stress to the rigors of keeping up a long story up. Planning out and writing in arcs can go a long way to prevent the burnout that epics tend to bring.
Be careful if writing a Genre Shift. A lighthearted romantic comedy could certainly become a chilling horror story, but have you foreshadowed the change? Is it internally consistent? Is it what the readers are expecting? Wham Episodes are all well and good, but if they come out of nowhere, your readership will likely be alienated. Also, provide honest content warnings.
Now some plot tweaks and useful tips.
Make other POVs of the same scene, like the mc saving someone, and a short pov of the one being saved. It's not mandatory, nor should it be done most of the time, but a few of them can really spice things up.
Show a villain's POV, about something mc will face in the future, a reaction to an event MC took part in.
Use flashbacks, when necessary, just don't go Naruto on us.
Everybody likes a good plot twist, whether they are a major or a minor one. Try making simple ones to start, like a good guy not having that righteous of motives behind his actions, etc.
Give the characters a conflict to struggle for, especially the MC. Whether they are traumas, internal reasons, dark past, current life problems, or anything. Show the readers said conflicts one time and just hint at them as events go by. Nothing major, unless something life-changing happens to them and said conflict.
Always have MC have someone to adventure or talk with, try avoiding making him too much of a loner. Not in the sense that he needs to have friends, but in the sense that he has people around him and lives in a truly living world. Even a NEET has to open the door and greet the delivery man.
(quora) Have the plot make sense. Having a good and steady plot is very important to the fic's likeability. Don't have the fic start as one thing and all of a sudden turn into another. it won't make sense, and will only confuse and annoy the reader. So, remember to stick with it.
Don't be afraid of emotion. Nowadays any speck of emotion is seen as a cringe. Ignore them entirely. They probably only want "big dick energy" or whatever. They are probably underage with zero experience on their belt.