What I suggest is to set up arcs. To me, setting up an arc allows me to explore certain concepts and introduce characters more easily without losing traction in the overall plot of my comic.

Lay your ideas out.
Ask yourself what you want the public to understand, discover and HOW you want them to understand and discover it.
Don't be afraid to put aside stuff, you can't fit everything in the story.

And if, after some brainstorm, you still don't know what to do, write a first draft for what comes after the beginning(what you're already sure of), don't be afraid of mistakes: it's the first draft.
If you see things you don't like in the first, start a second draft.

You could add a mcguffin: a story element that's not the main focus of the story but allows you to make it move.

For example in a movie you've got a cold war spy story with a focus on the love story of the two protagonists.
The cold war is the mcguffin
The main focus is the relationship between the two characters.

What I do is I not only have beginning and endings decided for my comic, but individual chapter beginning and ends as well. I usually end up just improving the inbetween from there and restructuring as needed. One of my stories I have a very set, vague idea on how every chapter is supposed to begin and end, and the other I'll probably have to brainstorm further down the line, but the initial few chapters are solid. Enough that I easily get started on each chapter, and enough to go through before I need to start worrying about those chapters that are more in the dark. I've honestly moved major events around in one of my comics already so what was originally chapter 2 is now chapter 3 and so on and so fourth, it's just whatever I feel serves the story better at the time.

I think using those characters you want to introduce as a starting point for story arcs would be a good idea, and from there, ranking which ones are the most developed/you're most excited about/etc. If I'm recalling correctly, your story is based on Alice in Wonderland, right? The books and films (well, besides the tim burton ones), are very heavily "introduce a character, alice hangs with character for a bit, alice moves on" so I think following a similar structure would work for your comic, using said character arcs to move you towards the ending.

SO YEAH that's my advice and how I'd handle it.

I have the same problem you have, a beginning and an end and vague hand waving in the middle. I have resigned myself to the fact that as I have written out the first half of my story the ending is starting to change, and it serves the characters better.

I started (as NeonBagel suggested) by creating arcs with clearly defined purposes. Arc one introduces the characters and the stakes, arc two up the stakes introduce some backstory. From there I broke it down into chapters, again with a clearly defined purpose. Chapter 1 introduce each main character and the catalyst for the story. I found that as I wrote the characters their actions became clearer.

Then I kept breaking it down with one or two sentences that describes what is happening. So it ends up like tree roots and then it is just connecting the pieces and scenes together. It also allows me to cut out things that don't push the story forward or move towards the end goal. Each scene has to have a one sentence description that gives value to the reader. If I can't come up with something then it gets rethought or omitted. I even break it down per page since I am doing a weekly webcomic. I do all of that before I even start actually writing dialogue. I find that it is easy to throw away things that aren't working if you haven't spent a lot of time figuring actually writing specifics.

This is known in writing as "The Great Swampy Middle" and it's an EXTREMELY common problem!

Here's a very small thing that made a big difference for me -- I previously tried to write out my drafts/outlines like this:

The problem with this is that everything feels disconnected. It's hard to determine what order things should happen in, or how to move from one idea to the next. I had a problem with my stories being more of an arbitrary series of events.

Then I saw someone else scribbling out their outline like this:

The difference is just a couple arrows, but thinking about it this way made a lot of difference for me. "I want this thing to happen somewhere in the middle" becomes "okay, how can this become a consequences of the choices the protagonists made in earlier scenes?" or "What event/scene/choice/etc. could lead to this happening?" and "What effects and consequences will this have on the rest of the story?" which all gives better ideas of where different ideas fit. Attempting to jot down my ideas in this way doesn't ever give me a nice, neat plot right away -- in fact, it's always been full of holes and questions -- but it did give me more useful questions to ask myself.

Like, don't get me wrong, plotting is still EXTREMELY HARD and probably always will be, so man, don't feel bad if it takes you a lot of work and a lot of iterations. But, in case it's helpful for you, too, I thought I'd share that little tidbit!!

I definitely have trouble with this too! I have pages and pages of ideas that I really like but have no idea how they fit into the over all story.

If you have a bunch of arcs/scenes written but aren't sure what order they go in, consider characterization. How would your characters be feeling and acting during these events, and how would actions and reactions be different if this scene happened toward the beginning of the story? The end? For example, if your herione encounters the bad, intimidating villain towards the beginning of the story, she'll behave a lot differently than she will after a whole story's worth of character development, during which she's had training and become much more brave and confident.

Also (and I guess this is basically what @shazzbaa said) think about if certain scenes build upon each other. A story is usually more engaging when it's not just composed of a series of unrelated events, but a series of cause and effect. The choices the main character makes in scene one effect what happens in scene two, which then lead him to make more choices, which then cause more events, and so on. If your scenes don't seem like they have these sort of connections, try tweaking certain aspects of them to see if you can make them connect more. I get really attached to ideas and don't want to change them, but often I'm surprised by how much more I like the changes I reluctantly make!

Sometimes, as painful as it is, you just have to remove a scene you really like because it just isn't working with the over all narrative. It's a natural part of writing. If you're still really attached to the scene after removing it, you can always turn it into a bonus comic or something, or even fit it into a sequel to your comic, if you ever plan on writing one (this has happened to me, i have scenes planned out for sequels to my comic, but who knows if I'll ever actually get to those!)

Also, even when you get to the point where you have things more planned out, don't be afraid keep changing things. As you continue to work on your comic and get to know your characters and world better, certain details may make more or less sense than they used to, so it's perfectly okay to change scenes that haven't been in the comic yet. I find that constant change really exciting, actually! If the whole story was completely set in stone, with nothing to figure out along the way, working on comic would get a bit boring and tedious, I think.

I know figuring out plot is hard and intimidating and frustrating, but I'm pretty sure we all feel that way, so don't give up! Just keep writing. You'll be surprised by how many ideas you come up with and connections you make while actually writing that you wouldn't have thought of if you'd just sat there brainstorming. Best of luck!

An important thing to remember in good storytelling is that every moment has some immediate purpose for the final outcome, whether it's directly related to the core resolution or related to the characters' arcs, worldbuilding, etc. Whatever you put in the "middle" of your story should be material that will strengthen and make the emotional impact of your ending much stronger. Including subplots, such as a characters' individual goal that may not be directly related to the main plot, or having a character process some kind of trauma, maybe a romantic kindling, etc--most successful stories have something called an "A" story and a "B" story, which you can read more about here1. Some stories even have C, D, E, F, G, etc etc stories!

TL;DR: Make a list of things that MUST happen in order for the end of the story to make sense, come up with ways to address those things as quickly as you can, yup.

A lot of people here have already said what I was going to say! Like Dojo, I take an episodic approach— working each chapter out like its own little mini-arc. That's also what I did with my practice comic and not only did it help me shape the story's middle in a coherent but exciting way, I think it's also really good training in general for story writing because you have to work on all these mini-stories all the hecking time.

The MOST IMPORTANT thing I learned from my practice comic was to get from your beginning to your end as quickly as possible. Don't add padding just for the sake of having a middle. It's easiest to write the middle when each "episode" or scene has a definitive point… so I made a list of all the information that had to be relayed for the end to make sense, and all the actions that had to happen to get the characters closer to their ends as well. Sometimes that was as vague as "X is revealed to be a cyborg". That was a HUUUUGE plot detail that I knew had to be addressed, but for a lot of my comic I didn't know how it would work out.

So before writing each chapter, I would pick a couple of the things that had to be addressed in order to get to the end, and I would figure out a few ways to achieve those things. So for my cyborg reveal? It was a big enough deal that I ended up writing an entire chapter just dealing with that. But since the cyborg thing had been on my list the whole way through, I'd been dropping hits for a long time before the chapter happened! And while I was doing my cyborg chapter I also managed to include several other things on my list, like "the police are tracking Y", "Z's sister is a wrestler and is looking for him", and "this world has a very advanced computer system but it convolutes security protocol". All things that I needed to be revealed in order for the end to make sense.

Before writing things this way, I always had a lot of trouble with middles because I knew they needed to be longish but I had no ideas what useful stuff to put in them, so they just meandered around without a point. It's actually SO MUCH easier to write now, because even though I still have to come up with the middle stuff, I know what the point of it is.

@Wishjacked Has most of this covered, as does everyone else, but I'll add that what really helped me was forcing myself to break my story up into 'elements' and figure out what happens to each one.

We're all aware that characters needs development and the plot has to move forward, so if you consider each character, plot element, and devise a 'thread' you need to make sure you can pick up and follow each thread individually from the beginning of the story to the end. Like, if you removed all other aspects of the tale, what would the story of that one character or arc look like?

If you pick up a Harry Potter book for example, and open it at a random page, you can pretty much take any character we've already met and have a fair idea as to where they are and what they're doing at that point regardless of what Harry and the gang are up to. We know these things because Harry is forever receiving letters, hearing conversations, stumbling on secrets etc. etc, and generally being a nosy little so and so, and that's what the middle is all about- cluing readers in to what everyone is doing in weird and usual ways.

So all those ideas you're coming up with are actually very valuable and may be just what you need. Open a document and get those things stored. It's gold, I tell you. GOLD.

Next, decide what the 'story' of each of your elements is i.e. what happens to that one character, even if they're off-stage most of the time? Example: there's a secondary character in my story who helps our heroes along but also learns to relax. Simple stuff, but whatever it is you come up with make sure that in each chapter, episode, or installment of your story there's a pinch of that mini-story inside it. Or at the very least make sure that at some point, if I really took a liking to a minor character in your story, I'd be given some kind of idea as to what happens to them when their part is over.

So...you know that in the first arc (chapter?) of your story these things are meant to happen:

So, does the main have friends who are going to see her housing the enemy and take issue with it? Might one of them tell someone else out of concern? Boom, well-meaning betrayal.

What is the main questioning about the world around her? Is it whether she can trust the people she knows, or if they have all the facts? What could prompt her to wonder this? It could be as simple as an anonymous message telling her to reconsider her friends, or seeing someone she trusted do something she never thought they would.

What's the cause of her premonitions? Can anyone have them? Does having premonitions incriminate her in some way? What if she's accused of spreading the madness by people who don't believe her? I mean, how else could she know who's going to get it?

Stir that pot and stir it good. It doesn't have to be complicated but it needs to be logical, at least from a character perspective. You can do loads of exciting stuff. Play around.