Yeah, so after playing through the campaign and multiplayer a countless bunches of times, I always noticed that in Container City, the thing that the security has to extract and get its a "bioweapon," yet if I end up on the resistance, they will say it's a "cure" to sickness in the slums or what not. So it always got me confused, was Captain Mokoena telling them that it was a bioweapon so the people on the security would be more motivated to steal it (because they'd probably less eager to if it was a cure), or is the the opposite way around and Chen told the resistance it was a cure. Was it just because the campaign plot lines are different, or was it intentional to make us wonder who is at fault and who is "good" or not? Thoughts?

I think this is exactly what the people who wrote the story for Brink were going for. It makes for great drama when the antagonist/protagonist arent distinctly defined.

neither is right neither is wrong, both have their reasons, and both believe they are fighting for what is best for the ark

Ah, would make sense, real war doesn't have good guys and bad guys.

I think most of this comes from crappy intelligence and miscommunication.

I mean heck just look at the resistance, they didn't even know they were bluffing. (reactor)

Yeah, I loved that moment in the last mission of the campaign, it felt the most dramatic of all the mission endings.
It'd be interesting if they ever make what-if missions of the war in the Ark after the reactor got blown up.

Reactor What-If part 2: Fight against Leukemia

Yeah that would be depressing.

Yeah, that would be indeed

The Security. (In my opinion.)
It's proven time and time again that they're willing to go to far. It may seem like a cure, but it could be trying to weaponize the problem so they can 'share' with the Founders.

As for Resistance, it could be legitimate, but I take everything they say or do with a grain of salt.

Despite my loyalty to the Resistance (and their awesome clothing), Chen seems to be telling lies, and is also a bit loco. Heck, both Chen and Mokoena are a bit crazy, but at least Mokoena tells his troops whats up. A good example of this is on refuel, when he finally tells them that there is a hostile outside world, and if the Resistance revealed their position, they would all be doomed. Or on Shipyard, when Chen says that the Ark has nobody inside, and is just a big showcase. If Security fails, Mokoena will repeatedly ask if the tower was evacuated, meaning that there are in fact people inside.

Here's a bit of wisdom from Fallout 3 for you:

"War is not about who is right- only who is left."

You make some damn good points...and love the FO3 quote lol