One of the challenges of writing a superhero comic book which reflects and is inspired my own life is that the genre demands lots of high-energy conflict, while the source material is mercifully thin in that regard. The way I usually address this is to write the inner and interpersonal conflicts realistically, and then let the super-battles grow out of them. And then sometimes the plot and the genre just demand some fights. So, sometimes I just do some fights.
For example, at the end of issue 13 I needed to show that the bad guy plan was bearing fruit. I needed to show that they were starting to beat heroes. So, what better way to show this than to have them take down the until-now invulnerable Sidekick? The scene work pretty well, as he is in one move, not only defeated physically, but also emotionally. He has never been hurt before. Relatively minor injuries open him up to the terror of vulnerability that everyone else deals with every day. For a scene which is essentially a plot point, it packs some punch.
Plus, it promises a heart-wrenching scene between Sidekick and Flamethrower. She has never seen him hurt before, and this new potential fear is something that they will have to work through together. Not really allegorical, but a nice scene.
And then the other day I was talking with my boss about the dangerous environment in which we work. After being punched by a student, I had to deal with the fact that I could actually get hurt here. That is scary for me, but it is far scarier for the people who love me. For example, my girlfriend.
What I thought I was writing as side-plot to advance the main story.... turns out was a pretty straight-up allegory for a very challenging dilemma I am currently facing.