I have had to play the story of the man holding a gun at the end of the world countless times, and have been asked to believe in it, to emotionally invest, to take it seriously. It is stark, bleak, exhausting, that I had to wait this long to see that experience done well.
Naughty Dog's The Last of Us is the third game in the last year to star a tough male hero in a paternal dynamic with a younger female companion character (Telltale's The Walking Dead and Irrational's BioShock Infinite are the others). All three games seem prominently interested in emotional narratives, and two focus specifically on storytelling in a post-apocalyptic world beset by zombies.
It's hard to call Infinite, riddled with "what not to do"s and benefiting little from its coin-flicking, improbably-waisted Disney caricature of a companion an exemplar of storytelling or relationship design. 
Which makes sense: as the game industry grows and stabilizes, the men playing and making commercial video games now have children and families of their own and have presumably matured as regards their acquisitive attitude to status and sex (or at least some of them have).
They may have developed a conscience about doing work that they can share with the wider world, rather than that illuminates a private power fantasy. The girls on the screen are now more reminiscent of daughters than of potential mates, and adult creators may now be experiencing a parent's sort of horror at putting those girls' fates into the grabby hands of young men of the sort they once were.
Post-apocalypse, as a genre, generally becomes about how men are to negotiate their social roles as the world's known structure becomes senseless. In eras of economic comfort (or confusion), the post-apocalypse fiction seems to be popular a values correction, reminding participants of the nobility of survival.
Zombie apocalypse -- a sort of crossbreed of the horror genre with survival fiction -- is an interesting one, though, specifically dealing with a redefinition and re-examination of what constitutes humanity's social and gender roles for everyone. "Loss of self," (represented as shambling infection) is the ultimate end to be feared.
That's thought-provoking given the adjustment many in games are trying to make toward a more diverse and inclusive medium and business -- and the anxiety a lot of traditionalists seem to express about the change that's needed in their culture. Note that among the three games discussed here that involve men as caregivers for children, the mother is never present.
BioShock Infinite presents an actual undead ghoul as a stand-in for mother; The Walking Dead reveals an infected (unfit) mother for a child presumed abandoned. There are two children in The Last of Us whose mothers are never introduced nor prominently explained. Games may be anxious about fatherhood, but on motherhood they're at a loss altogether, a fascinating dichotomy.
If you are good at the game, it lets you be good at it, and if you are not so good, the partner characters will actually help you. They react in plausible ways to things that are happening. If you have to play a partner-shooter, this seems like a wonderful thing to be able to expect. Your partners do not generally toss Witty Banter into gunfights, and instead save their words in those situations for warning you about things that are actually sneaking up on you.
Complicated times
But what it shares with the others is a certain anxiety about the man in games' role shifting -- once the young, muscular striver aiming to procure himself a pneumatic woman-prize through heroic deeds, his tenor is now complicated by age and the times. In this Guardian article, Keith Stuart discusses the rise of male-centric dystopia in games. He notes that while post-apocalypses are popular provocative story engines in games, they're still primarily focused on the role of the man performing necessary violence and exploring the job of fatherhood.
'It is on its face a video game, made to present specifications'
But while the spirit and culture of games is shifting, the fundamental structure and best practices of video games is slower to evolve. Popular commercial games need to feature certain familiar touchstones, either because marketing says so or because most people aren't used to making anything else: A character experiences a narrative event, shoots their way to the next narrative event, accompanied by high production values and melodrama. We see a lot of the world over a man's shoulder, we look often at his brawny, bandaged, armed pair of hands. Here is a description of The Last of Us: When the zombie apocalypse breaks out, you are a tough, bad-ass man of few words whose young teen daughter is tragically killed before your eyes by the forces that were supposed to protect you. Twenty years later you and your tough, bad-ass woman partner are smugglers until you encounter a cool teen girl who might hold the secret to Saving Humanity if only you take her to the rebel hideout, and now you have to protect her. Will the world be saved? Can you kill a lot of zombies on the way? Will you have an emotional response to the partner AI like you're obviously supposed to? Find out in this third-person action game with guns, stealth and melee elements! In other words, it is on its face a video game, made to present specifications. Yet it’s the grace and restraint with which The Last of Us approaches such limitations that sets it well apart from any other game where you play a sullen man trundling along with a gun. It's not that it's reinvented video games, or invented much of anything overt -- it's "simply" that it takes the things video games are about right now, takes the things that video games seem to have to do, and solves the problems of previous attempts. It takes some basic and very reasonable requests about games of their sort and answers them. From here on, there are broad spoilers about the story. You probably ought not to be reading an in-depth critique of a game if you are very concerned about spoilers. If we must have paternal narratives where literally all the female characters sacrifice their agency in some way to the male hero by the end, we should have nuance -- we should at least be able to argue that we're intended to reflect on that theme. We should at least be able to argue that the female characters stood for something other than sexist caricatures. For once. If this is the story we have to tell and the format we have to use, it seems difficult to do any better than The Last of Us. It is harder and harder to find a narrative justification for why your character can gun down hundreds and hundreds of men and still be a lovable hero (a problem Naughty Dog itself has with its Uncharted series).Killing zombies, killing people
If you have to patch this problem with zombies -- subject matter for video games not just because the issues processed within zombie fiction are emotionally convenient for game developers, but because they are humanoid targets you can set in the real world -- at least make the zombies interesting. TLoU’s zombies are incredibly well-done, genuinely seeming like people suffering various stages of a maddening disease -- from intensely-aggressive and sobbing to faces erupted with spores, humanity gone. Fighting them is intense, overwhelming, often prohibitively so (for me). It often induces the precise breed of panic and disgust that seems appropriate for a civilian executing a living thing with a heavy weapon. Of course, you have to kill some real people in TLoU, too. Probably still a few too many. But you can use stealth any time, if you want to, and it’s a fully-fledged option, which doesn’t happen that often in games like this, and that is nice. And sometimes you just use stealth because it makes more sense, not because the game has automatically correlated tactics with your moral stance that may or may not put you at odds with the protagonist the game is trying to draw for you or the story it is trying to tell. Amazing.