When a bio-terrorist’s engineered plague infects a superhero, he breaks out of prison to create a cure for the woman he loves.

>>?"it turns out to be the only way to kill a superhero"
It's not the only way, it's just that a villain who modified it modified is specifically so the superhero's known abilities wouldn't be able to counter it. (the plague itself wasn't meant to be a plague, and in fact plague is the wrong word but I didn't know exactly what it was when I started.)
But yes, the thing she created is the thing that is killing the man she loves. The concept is simpler than what people seem to be taking it for, but that's because I included 'superhero'.

So the central conceit of the story, the inciting incident, is an irony, that a woman bioengineers a plague (for whatever reason) ?that has an unintended consequence: it turns out to be the only way to kill a superhero, her ex-boyfriend, the man she still loves?

So the central conceit of the story, the inciting incident, is an irony, that a woman bioengineers a plague (for whatever reason) ?that has an unintended consequence: it turns out to be the only way to kill a superhero, her ex-boyfriend, the man she still loves?

>"I'm not sure why this needs a ?superhero?"
It doesn't really 'need' a superhero, but that's the world that she lives in. One with heroes and villains.
>", how about making the engineered plague the thing which gives the superhero his powers.?Thus, in order to save the woman he loves, he would have to lose his superpowers."
That changes the story. The story is about a woman who fell in love with a superhero, one of the world's greatest, and then an action she did causes him to only have 3 days to live. The woman then goes to any length to save him. And besides, the plague was created for a purpose that is completely different from what you suggest. (not that you could know from this logline).
So, again, it's not the superhero's story, it's the story of a woman who is trying to redeem herself, because she let herself become one very villains he had to stop.

I'm not sure why this needs a 'superhero' - it seems like a straightforward story of a guy's invention getting out hand and threatening someone he loves - almost like a Frankenstein thing.

However......
If you really want to introduce a superhero element, how about making the engineered plague the thing which gives the superhero his powers? Thus, in order to save the woman he loves, he would have to lose his superpowers.

And if you want to make a franchise, in the sequel you could create a way to restore his powers but with a constant threat to his life (a la Iron Man).

Ah, that's what I thought but I just wasn't sure. Okay, the gender isn't really important to the story. My original intent was to make him an African American man, which in fantasy/sci-fi are usually in non-important roles, or stereotypes. Or quite often stereotypical minor roles.
One last comment, I always like a good standalone story, everything is turning into franchises now, rather than giving new(and more diverse) characters their chance to have their story told. Anyway, it is a world filled with superheroes and powered people, that does suggest it could easily be a franchise.
Anyway, onto the story. While the points you bring up are things should definitely be answered, most of them probably shouldn't be included in the logline, but if you're curious I'll explain a little. The superhero does have superpowers, but she isn't immune to diseases. And there are more superheroes than her, which is why in my first version I referred to her as the "world's greatest superhero", so not everyone else is normal. As for how she gets infected in the first place, I will say that a villain got a hold of the plague and modified it to rid him/herself of this hero, but the MC still is guilty because he created such a deadly plague in the first place.
And the last thing, he does commit a terrorist attack by releasing the plague, and he goes to prison for that reason, but again I think saying that he breaks out of prison is enough for the logline. As for why he engineered the plague, I haven't the foggiest clue yet.
I do agree, that the story that is presented as her backstory in this logline is a story in itself.

Revision: When a bio-terrorist's engineered plague is modified to infect a superhero, the convict breaks out of prison to create a cure for the hero?she loves.