I am writing a fantasy series where the protagonist's main flaw is that she feels she doesn't deserve happiness. In the mid point, the protagonist and the antagonist come face-to-face and the antagonist is revealed to be the protagonist's ex, whose heart she broke. The antagonist gives the protagonist a clear shot to kill them and win, but the protagonist is unable to muster the strength to do so, because they feel guilty for breaking the protagonist's heart, and feels she doesn't deserve to win. Therefore, the antagonist escapes with what they wanted to accomplish in that specific chapter. However, I am not sure how my protagonist learns that she IS worthy of happiness and to NOT let guilt destroy her. I thought about her consuming a potion which makes her come face-to-face with illusions of all the mechanisms, people, groups etc. which ever harmed her, therefore helping her gain empathy for herself, but I don't feel strongly about it and it halts the plot. What do I do?
Plot is the dramatization of the lessons the character learns. So, if you have to pause the plot for the character to learn a lesson, something has gotten out of sync. "Show, don't tell" may be overused, not-always-applicable advice for novels, but when it comes to life lessons, it's non-negotiable.
The problem is that you want your character to learn that she deserves happiness, but nothing in the plot is leading her to that realization. Shoehorning it in isn't going to work. Either change the character arc, or change the plot. Maybe there's some other lesson she needs to learn instead. Or maybe different things need to happen to her.
Some possibilities: She might "earn" her happiness, by accomplishing something that is significantly good. Or she might get over her guilt if she learns --for instance --that her ex was manipulating her all along. Or, she might see a hero of hers try and fail and try again, and realize no one is perfect.
Message via story
Your intuition is probably right.
The best way to convey a message is via Story. The choices of people, plot and setting should/will/may tie into a message.
I would continue working with scenes and action, and stay clear of the magic potions for a little longer.
The best way to convey a message is by not giving the reader anything that even remotely looks like a message.
You need to tread cautiously. A too pronounced message will read like you're on a soapbox or preaching and readers will feel manipulated. You do not want that.
One way to go is to just finish the manuscript in a way that feels logical with actions the characters would perform and then see what message, story, drama, and tension can be found or cautiously tweaked out in editing.
Let the story tell you what it is about rather than trying to push it too hard into a frame. That's sometimes what even the most accomplished authors have to do (and some of them do it that way every time!)
Don't be afraid to kill your darlings! (In this case; the message, if that would happen to not fit into what you finish...)
For instance, when I read your midpoint situation it seems to me that it's rather about if you should let hate take over and kill someone or not. If your character had taken the opportunity to kill she would have followed a dark path (negative arc), while now, that she chooses not to, she can follow a positive change arc as someone that doesn't kill (especially old exes...)
If you want the message to be about happiness and a character's inability to find that for themselves, the midpoint should be about that.
An example of what you could place around the mid-point of your story:
One or several scenes where the character...
- ...realizes she has prevented herself from gaining happiness (A moment of truth).
- ...sees herself as if in a mirror (not necessarily any form of reflective surface... maybe she sees herself mirrored in the antagonist?) and realizes what kind of future she will have with no change: she has to make changes to find happiness! (A mirror moment)
- ...faces a choice between a morally bad and morally good action... in this case, where we're talking about happiness it's probably about her being good or bad to herself. A choice between some form of self-hurt or self-healing. (A moment of grace)
In the mid-point, the character decides, no more unhappiness. She goes from being reactive to proactive (if the story has a positive ending), she starts making plans, armed with the above knowledge.
This is her need; to be happy or obtain what makes her happy...
But there's the plan
From early in the story the character has committed to some plan, a response to the first plot point perhaps, and probably in such a way that she can't just up and walk away, there's money, reputation, or similar invested in the plan.
However, the plan is the total opposite of her needs. In this case, it will make her unhappy, it will remove her from what makes her happy...
This tension between her need and her plans (maybe even with some grumpy coconspirators less than eager to go for "happiness instead of gold") is what will fill the second half of the novel (inner conflict), together with the outer conflict (sword fights, horse chases, defeating the evil one, etc!)