I'd hate to disagree with my esteemed colleague Dreadmaker, but the case cannot contain 100% water unless you assume that the case itself is made buoyant materials like foam. To me the case seems to be made of plastic or at least metal, meaning that if water is the payload, the case will need to be at least partially air to make the case neutrally buoyant.
If, however, this was the case, we'd see the case moving around on the ground as the water inside sloshes. We'd also notice a drunken waver in any character as they move, with the water sloshing about. Finally, the case, if full of water, would be quite heavy; 20-30 lbs. However, the Scout can still double jump with one strapped to his back.
It's quite obvious that the intel is nothing but a flag to be carried; the same companies who can build giant rockets and bomb carts, portable mini guns and cloaking devices can't figure out how to move a briefcase on the ground if it's the same color as you are?
Also, both teams use the exact same technologies, and the exact same uniforms, differing only in color.
As a final piece of evidence, both RED and BLU are run by the same insane female CEO. You can hear her over the loudspeakers in both camps, signalling to both teams. Elated and angry with both teams at the same time. And, in fact, in larger maps you can hear her quite happily cackling as each team kills the other one.
No, I believe that both Reliable Excavation and Demolition, and Builders League United are both corporate fronts for a larger and more sinister corporation, run by a meglomaniac who enjoys the destruction and death of war, therefore pitting her two corporate fronts into endless unendable war against each other powered by vast clone armies with futuristic technology.
I think the brief case is nothing but air, a blank paper vending machine, and a glitter dispenser, designed to be nothing but a football in an endless battle.