Ok I'll try to explain this how I saw it so bear with me as this is going to be long and somewhat confusing unless you have played all of the game, seen all of the endings (there are 2 endings and one of the endings has 3 outcomes based on how you treat the epilogue).
Konrad at the beginning of the game is dead. He killed himself two weeks prior (the last transmission). This is my theory based on the intels in his apartment and the fact that leading up to the tower there are several intels regarding his "final orders". He is not only not seen, but not even referenced by anyone else in the game but Walker. The people know he is dead which is why the CIA is able to make their move (more on that later).
As for the 33rd. The 33rd you are fighting throughout the game are the Damned 33rd. They are a group that split off during initial evacuation efforts when the bigger sandstorms hit and walled them in. The 33rd went to war with itself as to why they were actually in Dubai (Walker makes the same statement in the first chapter "I thought we were rescuing people"). Konrad, closed off from the rest of the world thanks to the sandstorm, wanted to save the people and in essence live out there until help arrived. The others wanted to get out of dodge and only survive. Basically screwing the people who lived there. Lugo and Adams both make asides as to the 33rd going to war with each other, but you can also see this when going to each of their respective bases as the US flag flies right in the Damned areas and upside down (signifying distress) in the loyalist areas. It's reversed from the immediate logical since Konrad's men were the ones not actually in distress. The Damned were the ones trying to escape the city with the Radioman's beacon again, more on that in a minute.
As for the remaining 33rd, in the last chapter when you reach the tower and the soldier states that we are the last of the 33rd. this is meaning, Konrad's remaining fighters. The others were executed in the area in I believe Chapter 6 (whatever chapter that you find the broken radio) that you see a bunch of guys in chairs tied up and those that were lined up against the wall. Their uniforms are different and match those in the tower. His final orders don't put Walker in charge per se, but he is the highest ranking officer remaining hence the soldiers who still respect the chain of command to ask what his orders are.
The others, the Damned 33rd were those with the Radioman and those at the beginning that you try to rescue. He was technically their leader as they got their orders from him (which is why they chase Walker and coompany), though they didn't really seem to have an actual infrastructure outside of his leadership. Walker makes several remarks about how the Radioman was not the kind of guy you wanted running around a city like this. He was apparently crazy in Kabul as well according to the intels. The Damned seemed to fight just to protect what they claimed was theirs. Now these folks were mainly fighting the Exiles who were made up of refugees, militia, and those from Dubai who were going to fight back. They didn't want to be oppressed or have martial law imposed on them. The civilians basically fighting back and these Exiles are the ones that attack his group in the first Chapter based on actions from the CIA.
Now here is where it gets even more confusing. Upon arrival into Dubai, there is talks of a ceasefire. From the random Radioman quotes over the airwaves and the one piece of intel at the Nest, Konrad was the one that orchestrated said ceasefire. All was technically at peace between the 2 factions with Konrad, staying away from both with his own private faction at the tower. Though unstable the city was somewhat functional until the CIA came in (or were already there based on one of Lugo's comments and their intel outpost, it isn't clear) and started picking at the scabs on both sides. They had agents working both sides (which is why the first agent was dealing with the Exiles chasing down Daniels) and Riggs pulling all of the strings. Their ultimate goal was to wipe the map with Dubai so the story doesn't get out of the Damned going rogue.
While Konrad had basically given up and was holding out with his loyal followers (they mention his loyal men twice in the game) in the tower, the CIA started events in motion to starve out and dehydrate the entire city hence the weird stashes of food you find and the whole of Chapter 10 in taking the water and destroying it.
All this takes place as Walker is slowly going insane from being shell shocked (the rescue soldiers in the epilogue mention this). Apparently all of this has brought back the misery of Kabul where he, Konrad, his unit, or a combination of the three apparently killed a bunch of civilians, which again, is not really clear. What happened in Kabul is somewhat of a mystery but I think that is the point though Walker was definitely in the middle of it. As Walker slowly descends into madness, he imagines Konrad as his person or figure to blame or justify what he is doing depending on how you are playing. He is essentially following on the same path that Konrad did when he entered Dubai for the first time. Walker was causing a split in his unit (which is why he imagines killing each of them at different points) and even in the last epilogue scene where you kill all of the rescuers of the evac team, he reiterates the "Welcome to Dubai" line from the beginning again, restarting the cycle. Basically, like Kabul, had Walker just followed his orders which Konrad even states to him during the final cutscene in Chapter 15, this would have been avoided.
In essence, Konrad and Walker were like the same person which is why Walker found it easy to blame him for everything. I'm assuming one of them, or both, killed a ton of civilians in Kabul which again, was part of what made Walker descend into madness.
In any event, the story of this game was truly amazing in its execution in order for this debate or these questions to even be asked. Not even counting in some of the messages that make you question what you are doing as a player, but just the overarching story of not only a 4 way fight between multiple factions and the CIA, but also the internal struggle of a man clearly going insane from the situation. Amazing game and while my summation of the events may be opinion, that is what I could make of the story pulling all of the pieces together from the intel and having played through it multiple times. I do think the whole story is meant to be partially vague for the player to actually question where the "line" actually is and how far one would go before they considered it crossed.
I think I hit the key points though and got the players right to hopefully clear up some confusion I've seen from folks here. While I may not be 100% of outcome as that is meant to be up to the player, the key figures and their motives are at least right based on the what the game has laid out so hopefully this helps for some clarity.
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