(Warning: This post is more interesting if you've watched the movie first. It's not strictly necessary to have done so though, as there will be spoilers.)
Our lead is an anthropomorphized fox, yes. But damn if he isn’t confident, clever, self-assured, dominant, and handsome. He knows what to do and how things should be done. His wife wants to take the shortcut, but come on, he knows that the scenic route is so much prettier. Horse fence or bridle path? Again, it's the façade of a choice. The bridle path puts you out right next to the squab shack.
He has an electrifying career as a bird thief, the art he’s been perfecting all his life. He waltzes through gates, walls, attack dogs, fox traps, pitchfork wielding farmers and more practically without a care in the world. He’s suave, charming, and did I say handsome? In short, he’s virtually the epitome of What-A-Fox-Ought-To-Be.
12 fox-years later some changes are apparent. We don’t encounter him on an adrenaline pumping heist, but rather in the midst of classical suburban mediocrity. He’s hung up his bird-thief’s hat (bandit hats make recurring appearances throughout the film) at his wife’s behest and now writes a byline for a local rag newspaper. His clothes are less bold, his hair’s gone faintly gray, he’s eating pancakes made in a kitchen, not catching and killing his breakfast. He’s become... domesticated.
Of course his wife loves this new existence. Their son is —indecipherable hand gesture— different, they live in a literal hole, and there’s nothing to interrupt the dull monotony of everydayness. Peaceful or suffocating? Each of the Foxy couple would answer differently.
The impetus for this domestication is the typical one. Mrs. Fox got pregnant. Mister is only the latest in a long, time-honored tradition of parental zombification. The fantastic is pacified and slowly euthanized, until what remains is a shell that walks, talks, earns a paycheck, and is decidedly not in any way whatsoever —indecipherable hand gesture— different.
Mr. Fox: I'm seven non-fox-years old now. My father died at seven and a half. I don't want to live in a hole anymore, and I'm going to do something about it.
This is the first major subtextual theme: You just can’t kill the Wild.
The plot advances when Mr. Fox moves the family out of their hole domicile and into new digs.
He tells his wife that he’s tired of feeling poor. An explanation that he knows she’ll understand, and so one that is safe for him to cognize. He isn’t tired of feeling poor, he’s tired of being Nothing. Tranquil suburban domesticity grates because he has tasted the Wild. Like a gambling addict, once you’ve felt the rush of high stakes you can’t go back to playing penny slots... come on!
He traded one master for another. When he was a high-flying Animal his masters were Death and Risk and his rewards were Glory and Euphoria and Eudaimonia. Now a Domestic, his master is Conformity (or more specifically, das Man) and his only reward a vegetable existence of TV dinners and petty drama.
What is the true reason he goes to see the tree house? Not poverty. Not quite escape from poverty. ‘Escape’ misses the vitality of the motive. He rebels against this new, unfantastic Mr. Fox. He subconsciously goes to see the tree because he’s looking for a way out. Literally shifting his physical location is just the first step.
Now all of this is subconscious of course. Mr. Fox could never actually entertain these thoughts. He’s loyal to his family and cares about his wife. He knows that any rebellion is, either implicitly or explicitly, not just against Domesticity but also against them in a way. His wife wants this life, she doesn’t want to see a return of the Fantastic (and thus dangerously Wild) Mr. Fox. To act towards that is to act against her.
Mr. Fox goes to see the tree house as an act of subconscious rebellion, a first step to rebecoming who he wants to be. He buys the house because of Boggis, Bunce, and Bean. The challenge is there to be met. The other animals feel fear when they see the three farmers. Mr. Fox sees Conquest.
This isn’t rational. He isn’t thinking clearly, or even thinking at all really. This is the old Mr. Fox. Not a domestic newspaper suburban grunt. Fantastic and Wild.
The family moves into their new tree house and something is different. Mr. Fox is more and more his old self. He begins a series of raids on the farmers. With clever tactics, daring, and bravado he bests each of them in turn.
His wife, noticing the suspicious and ineptly hidden activities (the fun is in the heisting, not the logistics) drops one of the best lines of the film:
If what I think is happening is happening... ... ... it better not be.
Notice that Mr. Fox isn’t afraid, at any point really, of the farmers. He’s terrified of wolves and his wife. Almost as elaborate as his daring nighttime raid plans are his plans to deceive his spouse. Mrs. Fox is the true danger, because she can’t be overcome with clever plots and skill. She, not Boggis, Bunce, and Bean, is the true manifestation of domestication. Literally in that she is a domestic, who runs a domicile, but also as the vector by which Mr. Fox is "leashed" so to speak.
So that’s the stage about 2/3rds of the way into the movie. There have been victories, setbacks, standoffs, etc., but Mr. Fox is Fantastic again. The Wild was extant, then comatose, and is now risen again. What’s left is to complete the arc, to close the circle and provide catharsis.
The farmers, human characters with all the grandiose technological inventions and resources of modernity at their disposal prove simply incapable of killing the Wild animals. Excavators, bombs, helicopters, guns, and even a corporate labor force all fail.
The true conflict in the film isn’t between the animals and the farmers, it’s between the Wild and the Domestic. The animals have a society which is a perfect imitation of the human world. There are newspapers, accountants, plumbers, lawyers, etc. They’ve become soft and incapable. Mr. Fox’s value to the animal community, the reason they accept him back even after his antics bring the wrath of the farmers down on them and nearly destroy everything, is because he is the most Wild out of all of them. There’s a scene where Mr. Fox is absent during a crisis and the animals have to figure out what to do. They can’t. Like chickens with their heads cut off (chickens and dogs are non-sentient in this movieverse. u/TracingWoodgrains has some interesting thoughts on that iirc) the other animals have been fully domestically mindkilled.
When acting Wild the animals become more of what they are. Mr. Fox (and to a lesser extent befitting their lesser degree of in-touchness with their inner Wild, the other animals) feels most alive when doing a very particular sort of thing. The standoff with the rabid beagle comes to mind, as does the initial heist of Boggins’ Chickens. That sort of thing is characterized by how close it brings them to their roots — to their essence.
Mr. Fox: I had no idea how we were going to get out of this jam, and then it hit me: what do foxes do better than any other animal?
At the end of the film comes this scene. Mr. Fox references a fear of wolves numerous times, mostly played for comedic effect. What can be so scary that even the Fantastic Mr. Fox is left terrified? The wolf phobia is the clearest representation of the Wild story arc.
To start with, Mr. Fox isn’t scared of wolves.
He’s afraid of what the wolf represents. Wolves are —indecipherable hand gesture— different. There is a tension between the domestic Vulpes vulpes and the Wild Fox.
(The Latin name, which the wolf is markedly unaware of, is multifaceted. It gives the animals a concreteness which helps block their dissolution into domesticity’s erasure, but at the same time it is a fundamentally domesticizing construct designed to fit pegs into holes.)
That tension is reflected in every part of Mr. Fox, and every conflict in the film is rooted in it. The carefree adrenaline chaser persona conflicts with the devoted family man. The playboy conflicts with the chaste husband. The chaste wife conflicts with the “town tart”. The violent and capable scrapper conflicts with the refined gentleman.
The wolf represents the ultimate triumph of Wildness. It speaks no language. Not french, latin, english, or any other tongue. It doesn’t make plans or worry about the weather. It doesn’t worry at all. It is a Hunter and a Beast and a Wild-Creature and that’s it.
What makes Mr. Fox Fantastic compared to every other character in the movie besides the wolf is his inner tension. The Wild has a stronger grip on him. It makes him dangerous and competent. He hasn’t given himself over to passivity, not entirely.
The wolf isn’t his fear, it’s his love. He wants, almost more than anything else, to be the wolf.
When finally brought snout to snout with an honest to God wolf... he finally resolves his inner tension with a simple raised fist of solidarity. Wolf and fox are brothers, he sees. There is no need to fear or yearn for the Wild when it is already your blood.
Mr. Fox: I have a phobia of wolves!
The wolf does not answer. It breathes heavily with its mouth open. Its teeth are long, sharp, and yellow. Its tongue hangs out, and its eyes are wild. Fox looks back at it with the identical expression for a minute, mesmerized -- then Fox closes his mouth and his eyes soften. Fox raises his paw in the air. The wolf blinks a few times. It raises its paw in the air. It turns away and trots off into the woods.
Fox says wistfully: What a beautiful creature. Wish him luck boys.