If you've been told your novel or creative non-fiction has a saggy middle - or you've a nasty suspicion yourself about it - you are absolutely not alone. It's a perennial problem. Writing a novel may simply be a matter of "beginning, muddle and end", but as you discover every time you download an unabridged audiobook, novels are very long, and so the middle muddle is also very long. "Saggy middle" is one of the diseases listed in my Fiction Editor's Pharmacopoeia, but I've decided it's high time I unpacked it in a bit more detail.
1) Saggy middles may have different causes
The stakes aren't rising steadily. "Stakes" are about both what we could win or gain if it all goes right, and what we could lose or suffer if it all goes wrong: the bigger the gap, the higher the stakes. If the things the reader's hoping will happen for your MC haven't got more necessary and more desirable, and the things the reader's fearing will happen for them haven't got more potentially disastrous, then the story sags, because it loses momentum.
Your character isn't still grappling with the need to change. A story starts when circumstances challenge a characters' ideas and plans, force them to respond in new ways both practically and mentally/emotionally. But to maintain momentum and keep the reader reading, after a while you'll have to pose new challenges for them, so your MC needs new information and must find new and different responses. In other words, keep thinking "Then - but - therefore - but - then - but - therefore - but...".
Your non-linear timeline isn't serving the story. Each time you switch from one strand to another, any saggy middle tendencies will be magnified because the reader is being asked to drop their emotional involvement in one thread, and rev up their commitment to the other. So you'll need to work the structure of how the strands interact - what comes after what, where exactly you stop a scene, and where you start the next one - to maximise the narrative tension. If you repeatedly "cheat" by switching away purely to withold the the outcome of an event, readers will sense you doing that: you need to find a moment which is both a satisfying pause, and holds out the promise that when we come back later, Things Will Happen. More about non-linear timelines and switching between them here .
A zingy opening in medias res has postponed explaining apparently necessary backstory or sidestory until later. Now things have slowed to a crawl as you try to draw together the "now" of the story with all the material which explains and supports it. First, it's worth reviewing how much backstory the reader actually needs: it's probably much less than you needed to write in order to work out the story. Then stringently each scene in the saggy middle, to see if you can bring out, or add, things which build tension and momentum in the "now" of the story.
2) The Midpoint is crucial
Crime writer and writing tutor Caroline Greene talks about the midpoint as the tent-pole which holds up the whole story structure: indeed, what I would call Act 3 (of 5), she reckons is just that single, crucial midpoint scene. Essentially, it's the big turning-point in the centre of the story, when as a result of the main character's trying to get what they need and want, they act in a way that means nothing can be the same again. In The Godfather it's when Michael Corleone has to choose to take the gun out from behind the toilet cistern, and actually do the assassination. In Pride and Prejudice it's Mr Darcy's first proposal to Elizabeth: she is offered a splendid version of the husband-with-enough-money-to-keep-her, which is the only way she can survive in her world - and turns it down.
What they have in common is that the midpoint is a crux of the central issue that the book is about, which is present in the story right from the beginning; the very end of the story is where what started at the midpoint is finally resolved. Indeed, some writers start their novel by writing the midpoint, and work the beginning and end out from there. In Kim Hudson's antidote to the "Hero's Journey" kind of story-structure book, The Virgin's Promise, I think it's the "caught shining" stage. (I do recommend that book, particularly for stories where the central story is psychological: growing up or finding your authentic self, forging your true place in the world.)
3) A saggy middle is not necessarily about there being a lull in the physical action
What matters is that the characters are characters-in-action, and their actions are prompted by the constantly renewing and changing drive to act in the service of what they want or need. True, a powerful midpoint is unlikely to consist of someone lying down and having a snooze (unless your viewpoint character is Lady Macbeth, of course), but it doesn't have to be about an assassination either.
What's crucial is that whatever started your story off, your characters go on trying to get somewhere, action by action, scene by scene, until they find themselves at the crux which is the midpoint. Then, in the changed circumstances of the post-midpoint world, they must grapple with how they will go on. The best analogy I have for this is that of a ship's journey: the point is that every day of that journey, the character has to do something to keep trying to get somewhere.