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Start with an assassin, a person who kills.
Then delete everything you don't want him to be.
He is not a mad dog, a psycho or the dreaded emo guy who kills (which I will assume is a reference to Dexter). So he is not a victim of bad brain chemistry or a twisted personal psychology, yet he makes his living by ending other peoples' lives.
That leaves an enormous question hanging unanswered...

Why does he kill?

Sure, he might have taken the first few jobs for the money, but after that, with six or seven digits in the bank, there are a lot of easier careers to pursue. Yet he keeps
killing.

Find the answer to that question, and you will find out what distinguishes your dark gentleman from his murderous trope brethren.

My favorite answer to that question is that he is kind. He is a skilled murderer, with an unparalleled talent for painlessly transitioning his victims into the after life. He would be happy to quit, but he can't trust anyone else to do as good a job. He honestly cares for the quality of his victims life, right up to the moment that he reduces their quantity of remaining life to zero.

Establishing a conflicted character

My MC is in a dark line of work. He is an assassin.

Good start, a character in a dark line of work is assumed to be dark until told otherwise. Start with a murder; cold, ruthless and efficient murder. The character is firmly ingrained as dark in the readers mind.

He is also someone with lines he does not cross. He has been duped or coerced to do things he would not, but still holds to some standards.

Now there's some conflict. Is he a dark anti-hero content with his life or a hero waiting for redemption? Once you show the MC's humanity; mercy, compassion or a sense of guilt, readers will expect this to be a redemption story. He was dark but now is turning to the light.

The Throne of Glass series by Sarah J. Mass take this arc with an assassin in a fantasy setting. By the later books the character has lost most of what made them dark and is now a true hero rather than a dark anti-hero.

If I understand your question correctly the part you struggle with is: how to keep this character dark despite his redemptive characteristics?

Keeping them dark

To keep a character dark you need something else to make them dark beyond their line of work. This can be some character flaw, some secret to keep or a reason to reject opportunities for redemption. A truly dark character will, when give a chance to take a lighter path, choose to remain in the shadows.

Why does he continue to do this work despite the risk to his morals? Why stray so close to the line he swears he won't cross? Does he derive some sick pleasure from the risk or the thrill of the kill? Perhaps his line of work is his own compromise between his humanity and darker instincts.

I found a great article on writing dark characters that contains a lot of good tips. Among them is the following brilliant advice:

If you're aiming to create a "dark" character who will leave the audience unsettled in some way, remember: some of the best characters for this aren't the ones who leave the audience unsettled with them per se, but with themselves - because they make the audience realize that under the right circumstances, they could be those awful characters who do those horrible things.

Your MC's humanity and strict lines they won't cross are relatable, their methods are not. Keep it this way and your dark character will remain a dark character with a redemptive streak rather than a redeemed hero with a dark past.

What's in your MC's past, and what's driving him now?

Your MC is a professional assassin - a skilled murderer. Where did he learn his skills? How did he come to be in a position where people pay him to kill?

He has a violent background - but he's not just some street thug. Maybe he used to be a soldier (probably special forces of some kind)? His talents extend beyond just killing. He's a gentleman, someone charming. He's skilled at gathering information, too. So his superiors offered him a chance to serve his country in a different capacity - now he's an assassin for the CIA.

He believes in his country, and he knows that not all problems have peaceful solutions. Better one death now than hundreds or thousands later. He's a gentleman to his neighbors because they're the people he kills to protect. And he has a code: no unnecessary suffering, no random bystanders.

He's conflicted - why is that? Did he see something that made him think that the people giving him orders aren't entirely trustworthy, that maybe they're using him to further their own agendas? Does he secretly doubt that every kill he made served a higher purpose, and was truly necessary?

Keeping him dark - he's not crazy, and killing doesn't satisfy some sick need he has. But he stays in his job, so he doesn't hate it (or he's stuck). In my opinion, one of the most terrifying options is someone who kills and feels nothing. (He may even be surprised to learn this about himself.) He doesn't sympathize with his targets, but he doesn't hate them, either. They're targets, he doesn't see them as people. For him, killing is business and nothing more.

TL;DR, Give him the same personal traits as the here nameless human subject discussed in some of Anna Arendt's writings: a mediocre self-contented clown in need of constant approval from a group of peers he believes to belong to.

Also note that a human being that can justify to him/her-self the murdering of others by any ethical or moral paradigm would probably require a significant amount of cognitive dissonance, as probably was the case for some of the quirkiness of the subject of the book mentioned above.

Returning to A.A.'s book, and the implications for your character: you wish to create a character who commits monstrous acts and yet lives a normal life. The banality and sincerity (in contrast to making it up as an act of deception, e.g. as would be expected of a psychopath) of your character's normal life makes it difficult to perceive him as a monster, then we are left to suspect that he is some sort of clown. On the other hand, to call him a clown would make it harder for us to seriously accuse him of being a murderer.

While in real life we do not play lightly on this topic, in your book, you may decide where to trace the line. Simply bear in mind that the more sincerely and honestly normal your character believes himself to be, the less seriously he will be perceived as an assassin.

Now, to some details, freely borrowing from the book mentioned above:

• give your character a fixed set of moral guidelines, which he will refer to every now and then. Your character is unable to think for himself in terms of moral judgement, and has therefore to constantly rely on these mantra to justify himself. Ensure that these guidelines are:
  1) repeated mnemonically,
  2) copied from reasonable moral laws,
  3) stated in a manner that a normal person may agree with them.
  For instance "All jobs are alike, and all are in the service of society. Mine is like a cleaning man, like a trash operator, or like a factory worker." or "I do a service to society, removing the bad apples, and preserving the good ones, like a gardener, or a teacher."




• your character perceives himself as a "team-player". He has a constant need to feel part of the gang, to please the others with his efficiency, and to feel that his work has not let the rest of the team down. Make him suffer if he is left alone and without directions. By placing the organization above all else, he seriously impairs his ability to perceive the actual implications of what he is doing.




• while skilled, your MC should not be particularly intelligent. An intelligent assassin who wishes to live in the same society which he harms is by necessity mentally disturbed. On the other hand, make him reluctant to be tested, or to be faced with his shortcomings. Also, this will help make him unnoticeable, and anonymous, both of which are great traits to fulfill his dream of living amidst other human beings.




• Make him boast with his inferior about some of his results, which were not his to start with (e.g. stopping some dictator, or halting a war), and make him meek with his superiors. A clear understanding of the hierarchical ladder will help him fit into society too, obeying to (most of) the law, and even bringing it forward onto others, when given the authority.

While I have no advice on what you can do for your character, I want to suggest you go watch a movie called "Grosse Pointe Blank." The main character is a hired assassin who is looking to retire and is written in such a way to be likeable and pretty normal, aside from his line of work.

If you've ever seen the series "Transformers: Beast Wars" I highly recommend the relationship between the characters of Rattrap and Dinobot. At the start of the series, the former is a member of the Noble Maximals while the later is an evil Predicons. However, the loyalties are not static. By the end of the first story, Dinobot defects to the Maximals and a few episodes later, Rattrap switches sides as well. However, there is a distinction between the two that underlines their mutual distrust of each other (which over the series ranges from out and out hatred to just insulting each other because anything else would be cruel.). Where as Dinobot defects because he feels Megatron has dishonored their cause, and thus crossed a line, Rattrap defects because he feels it will benefit the Maximals.

Rattrap and Dinobot differ because Rattrap is a fanatic, but a fanatic for a good cause. If something can further the Maximal cause, but is morally questionable, Rattrap will not only justify it, he'll volunteer. For Dinobot, if something will further the Predicon but is morally questionable, it is better to side with the enemy than to comprimise on principals. Dinobot views Rattrap as fanatically loyal as the Predicons he just left, and thus, no better while he is a noble and honorbound warrior. Meanwhile, Rattrap views Dinobot as an oppertunisitic traitor to his kind, which is something Rattrap would only do if it meant his people would benfit in the long gun, he is the Patriot to Dinobot's spy with a convincing cover story. These dynamics are central to Dinobot's character arc, which build up to the final driving question: If Dinobot does not oppose the Predicons, his initial mission he started with in the very first episode will succeed... but he knows that such a choice has a major morally questionable price to pay.

Without spoiling, this conclusion to Dinobot's story is probably one of the darkest episodes in the Transformers franchise, let alone the Beast Wars series.