John Konrad did literally nothing wrongThroughout the game we're shown evidence of grave atrocities committed in the last six months in Dubai, but we are shown very little evidence that Konrad is personally responsible for any of it. My theory: Konrad and the 33rd started trying to keep order through relatively civil, but still martial law. Riggs and his CIA buddies didn't believe this would work, so they began massacring civilians that resisted and blaming it on the 33rd. Riggs isn't afraid the world will learn about KONRAD'S crimes, but his own. Konrad killed himself when he realized that he would be held accountable for the CIA's crimes.
John Konrad is directly related to Joseph Conrad by ancestryWhy then is his name spelled with a K? John decided to legally change the C to a K so that Walker wouldn't get the reference and be Genre Savvy about the themes that the game's story was borrowing from Heart of Darkness and Apocalypse Now. John Conrad was so Genre Savvy that he knew he had to make Walker Wrong Genre Savvy in order to succeed.
John Konrad is actually Captain Willard from the Vietnam WarCaptain Willard stayed with the American Military and eventually ranked up to Colonel, but after many years of service got so depressed from the trauma of having killed Colonel Kurtz so many years earlier that he tried going on many different missions to redeem himself. The events of Spec Ops The Line is just his last in a long line of failures, and now he has gone insane just as Colonel Kurtz, assassinated so many years before, had lost his mind.
The events of Uncharted are a continuation of Walker's delusional fantasyAfter he returned home to America Walker was psychologically evaluated and deemed unfit for duty. Ever since then he has been in a mental hospital imagining the events of the Uncharted series, as Nathan Drake is the idealized version of the action hero. Nathan Drake is basically Indiana Jones, with all the associated genius level knowledge on history, languages, archeology, etc. and cool-headed personality. Add in a little bit of spice from pretty much every action hero from the past 30 or so years and Nathan Drake is the perfect hero, Walker is realizing his fantasy of being a hero behind padded walls. However there is some good news, the ending of Uncharted 3 showed Nathan Drake settling down so this may be symbolic of Walker's hero fantasy settling down as well.
Alternatively, Walker and Nathan Drake are the same personOfficially speaking Nathan Drake doesn't exist, that is just a name that he chose to call himself. The identity of Captain Martin Walker could very well just be a cover identity he created in the U.S Military, the training of the Delta Force being relatively easy for him to adjust to given his athletic ability and stamina as seen in the Uncharted games, for the sake of cover operations where he needs to pose as a Military Officer. Uncharted 3 exposed Nathan Drake to some very heavy hallucinogens that gave him a bad Mind Screw, I say that the events of Spec Ops The Line is Nathan Drake suffering from dissociative disorder as a result of side effects from the drugs he was exposed to, only at the end of the story where he meets Konrad does the illusion finally shatter and he realizes it is time to go home and go back to being Nathan Drake.
Konrad was present in the story, even if not in the fleshThe representation of Konrad seen by Walker is not a hallucination but rather a ghost. The ghost of Konrad is haunting Walker until he can learn to come to terms with what he has done. Whether Walker decides to become the villain he thought Konrad was or to go home Konrad decides to leave Walker alone after that because he has finally made his choice.
Heavy Troopers are no more durable then regular soldiersThey only seem that way because Walker is missing due to his progressively unhinged nature and is rationalizing it as super human durability. The fact is no nation on earth has that many 8 foot tall soldiers who can absorb multiple direct hits from RPGs. The Heavy shows up frequently in Walker's more obvious hallucinations, culminating in the HaLugoNation. The first heavy also appears in after a horrific white phosphorous bombardment under poor visibility conditions. So rather than absorbing whole clips and multiple grenades, Walker is simply unhinged by something in the Heavy's appearance and can't shoot straight. It's possible that the Afghanistan incident involved an IED and Walker has bad associations with EOD workers. That or it's something we weren't keyed into by the game.
Walker killed the Radioman.The Radioman hasn't actually snapped from being in the city; unlike the soldiers, he can mostly keep to himself and not directly see the horrible things happening. Walker's state of mind is making the Radioman worse than he sounds when he broadcasts. This is why Lugo suddenly seems to break character in order to flatter the Radioman enough that he'll give them instructions on operating his equipment; Lugo should be more than smart enough to figure that out on his own, like he says he can earlier, especially considering the Radioman setting the mic to broadcast requires him to press all of two buttons. The scene we see of Lugo killing him is Walker filling it in with something different so, as usual, he can blame someone else for his actions.
Big Boss is Walker's fatherFurthermore Walker's full name is Martin Peace Walker.
The ending of Uncharted 3 is what led to Dubai's sand stormIn the ending of Uncharted 3 Ubar, an ancient lost civilization/city, collapses into the ground when Drake accidentally causes a chain reaction with just a few bullets. There is a possibility that the massive collapse of such a giant city sent shock waves across the landscape building up a sandstorm of apocalyptic proportions. Dubai isn't the only city that was affected by it but that just so happens to be where the sandstorm came to a standstill; it took so long to reach Dubai because there was so much devastation that the rest of the world has had its hand's full trying to rescue everyone. Consequently, if Nathan Drake really is Walker as stated above, then he is trying to redeem himself by saving Dubai.
The incident in Kabul was a case of friendly fire, required by the circumstancesWhat makes the White Phosphorous incident so terrible for Walker is the fact that the circumstances required him to use it, the size of the Damned 33rd gathered at the Gate made it impossible to handle them any other way. Those civilians that were burned to death were just a side effect of the fog of war, the circumstances forced his hand. In the same way I propose that back in Kabul Walker was forced to call in a danger close air strike to save his comrades from being overrun by the enemy, unfortunately allies and civilians were caught in the cross fire. In the aftermath of this air strike Colonel Konrad came onto the scene and rescued Walker who was too injured to continue fighting. When Colonel Konrad said that Captain Walker performed admirably under the circumstances he means that Walker had no other choice but to sacrifice the lives of others in order to save himself and that of his comrades. That is why Walker doesn't like to talk about the incident, he wishes that he had been strong enough to not have to use such tactics, and in the same way he wishes he never had to use the White Phosphorous.
Walker's apparent lampshading of the use of In Medias Res during the Once More with Clarity helicopter sequence is referring to his experiences in Kabul.By this stage Walker's mind is almost completely gone. Flying through Dubai in the helicopter reminds him of some incident in Afghanistan, and he's so messed up in the head that he can no longer tell the difference between the past and the present. Instructing Adams to fly into the sandstorm might, in his bizarre dream-logic, be an attempt to break out of the apparent "Groundhog Day" Loop he finds himself trapped in. As to why he does not say "we did this already" in the opening of the game might be chalked up to Unreliable Narrator.
If for some reason there is an Updated Re-release, the following things will be added:
In the "good" ending, Walker suffered no consequences for what he did.
At some point Walker started hallucinating about the Radioman
The Gray Fox Team was unaware of Riggs's plan
The Middle East would have never declared war on the US if the truth got out.
Walker is a figment of Konrad's imagination, not vice versa
Lugo and Adams didn't disobey Walker, because they thought they were the ones who were crazy