Mass Effect: The trap is sprung
As Shepard stood there looking at the three choices the catalyst had given her. She felt the pull to synthesize, or even to control the reapers. She took one step towards the blue core and raised her gun, but hesitated. The AI in the form of the boy from her dreams pushed her again saying, "we are running out of time you need to choose the new solution." Then it clicked the boy from her dreams, the AI's avatar, indoctrination, her thoughts muddled, the three choices, two would save, one would destroy, no there was another option as well.
She could let the fight play out, but the odds were not in their favor. But if she synthesized everyone they would basically be modified into reapers. To destroy them, she would have to destroy an entire race that had just made peace with their creators. She could control them, but with the thoughts of indoctrination, how can one who is indoctrinated control those controlling them? There are no good choices for her to take, but she could not take the choices that seem easiest because that would be letting them control her. So she changed her footing and raised her pistol and fired at the red fuse. Shooting repeatedly as she staggered towards the cracked fuse. As the Fuse sparked and started to blow she heard the catalyst say, "We are glad there was never really a choice for you." As the heat of the explosion washed over her the voice continued, "Why would our weapon design, which you built, be designed to hinder us?"
Authors note: This is a one shot.
This is a slight variation on the indoctrination theory, along with something that bugged me about the weapon they were working on to destroy the reapers. It was found in the prothean beacon on mars, a weapon they built but couldn't power. Meaning they were following the designs of a previous race. Then you find out the power source for it is the citadel. The only logical way that would work would be that it was created as a false failsafe incase a cycle managed to organize a resistance that could work. By them finding this weapon they would waste their resources building it. And it would not make sense for them to provide a way to destroy themselves.