Duke Nukem/WMG

The Franchise will be rebooted as a parody of itself.
Oh come on, if Duke Nukem ever gets a reboot, you KNOW it will basically be a parody of itself.
 * This doesn't seem to be the case if what's been seen of Gearbox's Duke Nukem Forever is to be believed.

Duke is insane and believes he is an action movie star; the "aliens" he sees and kills are normal people.
We only have his word for it that he's doing what he seems to be, and his speech is so peppered with quotes from other Badasses that it's hard to take him seriously as a rational figure.
 * Further evidence: He sees the Space Marine from Doom dying. Now, really, what could take out the Berserker Packing Man and a Half, but leave Nukem standing?
 * Also, he goes to death row. I have a hard time believing aliens would bother with an electric chair.
 * Why would the Pig Cops bother with the Cop shtick? Those are actual cops.
 * Mi-go, I could just see it now! You're playing the latest version of Duke Nukem. Generic FPS, shooting bad guys, you and your friend are high-fiving each other when you bring out the shotgun and watch the gratuitous gore go splat. All of a sudden, the entire game changes. You're no longer fighting aliens on a space ship, you're shooting at innocent people in a city. It'll be awesome! It'll piss off everyone! Media guardians will be angry because you'll be killing innocent people and gamers will be angry because all of a sudden the game got preachy (though it only got "preachy" by changing the models, rather than having somebody come on the screen and say "No. That's bad. Violence is terrible.").
 * The problem with that is that the aliens have clearly alien goals: namely they've kidnapped women and put them in slime...pod...things preparing to rape them later. If the Pig Cops were actually human, then that STILL would only make them corrupt psychotic rapist cops with scat fetishes who've taken over LA as their own military state. Unless there is some OTHER reason why "normal" cops would encase women in green shit and sexually assault them. And there is simply no way to explain the smaller slime monsters, the Octobrains, or the fact that if this were the case then Duke Nukem would have to literally be superhuman to take down an entire army so easily. Realistically, and ironically, the "they're aliens, and assholes" answer has fewer logical loopholes. It's possible the Doomguy was sent in first and Duke is his intended backup, too late to save his comrade unfortunately. An aside: the concept behind the Pig Cops is that they were, at one point, human cops who were mutated by the aliens to be enforcers...so one could still theorize they're "innocents" being killed by Duke, but only in the sense they're normal people enslaved by the aliens. Of course they were still kidnapping women to rape later and encasing them in slime, so they're probably still assholes anyway unless they're being mind-controlled too.
 * You're forgetting something, the women in the slime pods don't exist, they are a figment Duke's imagination.
 * It might have simply been a generic space marine. The Doomguy was sent with a bunch of them, and they all got killed.
 * This is further supported by the fact that parts of DN 3 D are inspired by They Live!, the plot of which is that a guy finds sunglasses that make him see the true nature of aliens disguised as people. Coincidentally Duke Nukem himself wears Sunglasses at Night.

Duke Nukem is a cyborg, or a robot.
He’s got balls of steel.

Duke Nukem used to be Johnny Bravo.
When the aliens invaded, Bravo decided it was time to man up and changed his name to Duke.

Duke Nukem always has been and always will be a Stealth Parody of America, sexism, action heroes, and the '90s.
It's just so over-the-top nobody takes the series seriously. Which is exactly what it wants you to do. And one day Duke is just going to come out of the screen to say: ""Whoa, you thought I was serious about all this?! You're an idiot!""

Oh, and because of this video. Boom, your mind is blown.