The logline doesn't say that the agent is a nothos. Unless the wording here "As the government struggles to contain a mutant species, the Homo nothos (false man), one of its federal agents" is what is confusing? I guess it does seem like "one of its" refers to the "mutant species" instead of "the government." I'll see about rewording that.
I didn't say that the protagonist won't have a love interest but that there isn't any romantic love between the agent and his partner. The designated "romantic interest" is actually the crime boss. Which is one of the reasons why my initial loglines focused on the agent and crime boss.
So to clarify (cause I feel like things are getting a bit jumbled):
The federal agent is human. His name is Rove.
His partner is a nothos. Her name is Eliza.
The crime boss is half-human, half-nothos. His name is Lux.
Rove and Eliza have a strained relationship but do also develop respect for each other. However, this does not stop Eliza from wanting her freedom, nor does it stop Rove from disliking/having issues with, the nothos. Now, I was thinking of that last logline (about the rebels) as them after their relationship has been established. However, that is easy enough to change. So, their partnership can be new, and begins just before they are given the task of infiltrating the rebel force. This offers more conflict, and can create more possibilities in Rove's backstory, e.g. exploring what happened to his old partner.
Rove and Lux have a business arrangement where they exchange information--Rove offers Lux a heads up about certain government activities, and Lux helps Rove take out other criminals--and they are also lovers. Lux would be very interested in taking down the rebels as well, since they are bad for business, but he also enjoys making life difficult for Rove, so he'd probably play both sides.
The idea of the rebels was a sudden inspiration and can be replaced with something else. However, the relationships between the characters--with the exception of the timing of their meeting/beginning which is mutable--is as stated above.
Perhaps it would be better for the logline to focus more on the development of the partnership of Rove and Eliza, and not on a rebel force since that might complicate matters too much. This logline--
In order to contain and cure a mutant species, the Homo nothos (false man), that threatens the survival of the human race, a federal agent must partner with one of their own, a female nothos bent on obtaining freedom.
--was more general in that way though would need to be reworked a bit still.
I understand that you like the clashing personalities vibe better, but that's actually what I was attempting to go for in the original logline with Rove and Lux.
Originally, the setup was that Rove and Eliza were already partners for about a year. Their relationship is tense, and she's beginning to rebel against his authority more and cause trouble, yet, they still work together well at times, which gives Rove hope that she won't actually run off. Eliza's biggest issue with Rove is that he's ignorant and doesn't understand her kind at all. Their relationship, the building of their mutual respect but the continuation of her pursuit of freedom, was to be the "B" story.
The "A" story was admittedly weak because I didn't really have a definite stakes in mind when I wrote the first logline. The "A" story is that Rove is tasked with investigating and removing a new threat to the organization responsible for handling all nothos matters (the Registry I mentioned in earlier versions). The threat is Lux. Rather than remove Lux however, Rove ends up fascinated by him and Rove starts an unsanctioned cat-and-mouse game where they sometimes help and sometimes betray each other. They also eventually develop a romantic interest in each other (my thought was this would happen by the end of the first season).
You asked about irony earlier. Honestly, the Rove/Lux relationship is an ironic twist. Especially because Lux's kind--the half-human half-nothos kind--are meant to be killed without question. They're considered an abomination. Which is a fact that would be explained quickly in the pilot and means that Rove is putting his career in serious jeopardy.
All that being said, I don't mind swapping the "A" and "B" story lines around, and having the focus be on Rove and Eliza's partnership. I would just like to figure out which relationship will get the prime spot so the rest of the premise--the stakes--can be decided, so I can complete the logline.
Any thoughts on all of that? Do you still feel that the Rove/Eliza relationship should go front-and-center?