No one starts with the themes when they're telling a story. Or at least no one has admitted to ever successfully writing a story that starts that way.
Themes emerge with time. It's a reason why you edit a story, because it gives you an opportunity to go through find those themes and strengthen them through iteration.
"Throughout the ages, stories with certain basic themes have recurred over and over, in widely disparate cultures; emerging like the goddess Venus from the sea of our unconscious." - Joan D. Vinge
Before we can address themes we have to know what they are and how they work.
In its simplest sense, and the one most people should be aware of from language or literature classes, a theme is a recurring idea. Themes occur, in literature, in two ways. 1) the repetition of a phrase, or 2) the reoccurrence of an image. In either case the idea being repeated does not have to copied exactly, but it can be.
In literature it's common to have themes examined from a number of perspectives. And the same holds true for other mediums. The exception there may be music, where a theme is often times a recognizable melody that is repeated. Star Wars and its themes for Darth Vader and other characters.
Video games being an amalgam of various mediums - cinema, literature, and music - undoubtedly can and should make use of all possible methods of introducing themes.
But at this point you may still be wondering what a theme in a video game looks like given their penchant for shooting or blowing stuff up. How can anyone say anything with that? Well... I won't immediately look at a game with shooting, but rather one that's quite overt in its themes - The Witcher 3.
There are others that we can find in side quests but it's these two that reoccur throughout the main story. Those themes are fatherhood and men versus women. Fatherhood is repeated thrice throughout the main story in various forms. Given the entire time Geralt is looking for his adopted daughter Ciri it's hard not say otherwise. But in his travels looking for Ciri he encounters the Bloody Baron.
The Baron is an absent, abusive father who is confronted by his misdeeds at the loss of his family and the rejection of his daughter. Fatherhood is quite literally what he relates to Geralt over, not violence, or war, or monsters. Fatherhood continues when Geralt goes to Skellige and meets Crach an Craite and his children Hjalmar, Cerys, Ragnar and Loki. Whereas the Bloody Baron was about the pain caused through fatherhood and the loss one can experience, Crach's quest line is about what one can pass on to children. It's about inheritance.
Every instance where Geralt encounters another father is one where the theme is reiterated and explored. All the dimensions of what it means to be a father are placed into the game from the responsibility, love, exasperation, hope and future that such an experience holds.
In game design especially when it comes to puzzle, enemy or level design it's common to iterate - to repeat an idea and see how it can be changed. Themes are no different.
That's why we see Geralt encounter other fathers who are having their own issues with their children. None of those problems is exactly the same, but they are of a theme. The story of Geralt and his search for Ciri need never have the Bloody Baron or Crach an Craite be fathers. They could equally have related to Geralt as men, warriors, drinkers, gamblers or other aspects of the world. But those other aspects would not have tied in to the story as well. Nor would they necessarily have provided as complex depictions of those characters as fatherhood does.
Fatherhood is a more common theme in games these days not just because game developers are aging and looking for new experiences that more closely relate to their lives, though that's part of it, but because it's an easy way to make the protagonist emotional vulnerable and mechanically impotent when they're a superpowered übermensch as they so often are in video games.
Just look at the most recent God of War, or The Last of Us before that, or even The Walking Dead. All three games deal with fatherhood in some sort, for better or worse. The Witcher 3 doesn't stick to just examining fatherhood, it examines gender and how the various genders relate to one another. It does this though Geralt's interactions with Ciri, Yennifer, Triss, Keira and the Crones of Crookback Bog.
The women in their stories and encounters with people other than Geralt also build upon this theme. And each in their own particular way. Ciri, obviously takes the position of daughter or child. Though clearly an adult and not a child physically or mentally, she may need Geralt's help regardless. For the greater part of the game the player is tasked with ascertaining Ciri's whereabouts and condition.
Yennefer and Triss share the position of lover or friend, depending on how you play out those potential romances. In each instance its Geralt who needs their help and only later through interacting with them and building on the player character's relationship do they need Geralt. Keira sits firmly in the middle of this spectrum of women in relation to Geralt as she is both a friend and a lover but someone who also needs his help.
That leaves us with the Crones of Crookback Bog, a trio of creatures that serve no purpose but their own. And whom both Ciri's and Geralt's encounters are nothing but antagonistic, if not always overtly so. Every one of these women, crones included, is treated as Geralt's equal. Yes he may have feelings for them, or feel protective, or even disagree with their choices but that does not mean he undermines them or otherwise put them down. He recognises in each that they have their strengths, weaknesses and areas of expertise where he does not.
This is readily contrasted by most other men in the game. Witch hunters, bandits, soldiers, druids, warriors and most other NPCs that attack anyone who can't be classified as a sentient being. The only males who don't seem to have it out actively for women happen to be the few friends of Geralt. But even the Wild Hunt, the spectral force which presents as male or masculine and is the titular antagonist of the game is after a woman - namely Ciri. They are another iteration of the male gender, at least in my armchair analysis as there's nothing explicit about the Wild Hunt having any gender beyond the body shape given to the characters.
Women take a big role in the life of Geralt and that's not to say we don't see him examining the role of men to men or men to a third or non-gendered person. The latter really only happens once with the elf Elihal, and even then its not explored in any great detail so I can say definitively what if any gender they prefer to go by.
I think by now you may get the point. Or at least see that the Witcher 3 has a lot going on with it and its story. The writing and narrative design are good because they iterate on an idea and not just a mechanic. Games, unlike other mediums, are composed of so much more, so many more ways that themes can be established and emphasised. It's not the writing alone, but colour palettes, art styles, musical scores, sound design, mechanics and systems integration, and just about every other aspect of a game that can support and strengthen a theme.
Sure the first and basest versions of them may occur, but that's the case for any medium. The first draft always has something worthwhile in it. It's why we rewrite and edit. Editing is iteration.
To do so successfully or well, since the two are not always the same, requires taking a step back. Not just from the script but the game. In the process of writing or designing it can be and is difficult to know what you have. Things automatically make sense in your head because you know what you mean. It takes no effort to describe to yourself what your intentions are. It's different when you're communicating with another person. So, as with all forms of communication, in writing we have to seek clarity and test to make sure.
Games are no different. By and large they've gotten really good at testing most aspects of them to see that they're working. It's why Destiny 2's gun combat can feel so fun and good. A weird concept when you stop to think that I am actively saying "it feels good to shoot someone in a video games." Games are not so good at testing the story. We don't have screenings like film does to see if it works for an audience. Of course even with film they're not always changing things to make movies comprehensible or logical.
Beyond self-examination and critical analysis at every stage. Every game is created in a different manner. By that I mean some games are created with a mechanic in mind, others want to evoke a feeling, and still others have a story to tell or at least an IP to use.
Whatever the case, it takes iteration and editing of the story to bring out the themes and hone them to something that speaks to players. That takes time, something to often not given to the story. Some themes exist without the need to do much work. Oppression and fighting are going to be inherent to any work dealing with the Nazis or fascism. Just look at Wolfenstein - you're quite literally trying to fight oppression.
But Machine Games went one further in the two latest versions - The New Order and The New Colossus - they didn't merely demonstrate the Nazis as being a force a soldier contends with but one society does. As fun as it can be to punch Nazis the games show you a world under the thumb of the Nazi regime and how everyone is affected for the worse by it. They made games where it's not just Allied soldiers who have to fight nazis but women, children, Africans and African-Americans, Jews, Christians, and even former Nazis as is the case of Klaus Kreutz who turned on them when his own son was killed by the Nazis for a birth defect.
This is further illustrated in The New Colossus when American Klu Klux Klan members, who are Nazi supporters, welcomed the Nazis regime to the US are being forced to convert to speaking German. Even in their own ostensible homeland white supremacists are being oppressed. Machine Games have done brilliantly at showing across two games how Fascism and oppression hit at home. They have written and emphasised a theme and message in such a way that the games reinforce it not just through the story but level design, sound design and world-building.
Mechanics is another issue. But it wouldn't be a Wolfenstein game if you weren't a Jewish superpowered übermensch. Which itself is clearly a knock at the idea of the übermensch being a strictly aryan ability.
That message can be explicit or implied. Or it can sit somewhere on the spectrum between the two. Where it is and how well it does of course will be determined by your writing. Themes will help convey a message. They will help a player understand what you as a writer or creator are trying to say, or the feeling you're hoping to impart. But they will only do so if you know what you're trying to say. But more on messaging in games on a future episode.
For now I figure I'll just end this with a mention of some of the themes in Firewatch and Gone Home, which are isolation, connection and the self. It's the same themes for them both. And no, I won't waste your time by arguing those points, you can always hit me up on Twitter if you want to know more.
Unlike the Witcher 3 or Wolfenstein, both Firewatch's and Gone Home's mechanics help to emphasize their themes. Now it's not always possible, based on the story of the game and its genre. If you want to tie a story's themes to other aspects of the game beyond just the narrative that's going to require two things - 1) the story is written at the beginning to allow for editing and iteration and 2) Those themes are communicated to the rest of the team so they are given the chance to explore them and in turn impact the narrative as well.