Let's face it. While this game somewhat tried to add something new to the franchise, the plot wasn't that good. It was actually bad. It was so full of holes it can easily be confused with Swiss cheese.
First, you have Jonathan Irons, who in an attempt to look as a complex and sympathetic villain, turns out to contradict himself more than once. For people who actually plan to buy this game SPOILERS AHEAD; He kills hundreds of thousands of soldiers in a biological attack and allows many others to die by hiding crucial intel, but actually refuses to kill the main protagonists because, and please don't laugh, he is not a monster. That's what he says before he leaves the room with the two people than can ruin his plan alive and well; "I'm not a monster."
I thought the rehashed scene where the antagonist nearly kills the protagonist only to be distracted long enough for the latter to gain the upper hand, which is present in most of the previous installments, was ridiculous, but this one is just outrageous.
Second, the way how the good guys find out about Irons' plans is too cheap. Basically, they fight this terrorist who has been playing the recurring antagonist 'till now, and he hands you a flash drive before he dies that shows Irons' killing a scientist in cold blood. How he caught that footage is never explained.
To describe it as simply as possible, the campaign of Call of Duty: Advanced Warfare is like a series of sequences of the good guys being cornered and then being allowed by the dumb antagonists to find a solution. It's like Star Wars all over again, without the good parts.