Question: What would the people outside of the wall gain by destroying the whole city? It was WCKD they were after, right?
Question: Why did Janson kill Ava Paige?
Answer: Because Janson wishes to be the one in charge. He plans to cure himself and only the people he deems worthy, presumably so he can "rule the world."
Question: Couldn't WCKD send armed troops to kill/capture Thomas (and the others) since he's so dangerous to them (before their tags got removed)? It's not like they don't know where he is as they could get the drone to follow him and show his whereabouts on their map.
Answer: Yes, they could have, but they didn't. Why? Go ask the movie director.
Answer: It's not so much that the rebels gain anything by destroying the city, it's just that they are untrained and driven by rage. They do not act as a military unit, they act more like a mob. They lack the discipline to strike only enemy combatants and instead cause chaos in the entire city. The point is that the rebels are acting no better, and in fact quite a bit worse, than the infected do.
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