I have a slightly different theory:
Instead of capturing Zygarde, it's like in Platinum where Cyrus ends up summoning both Dialga and Palkia, or in Emerald where both Kyogre and Groudon are set loose.
It even makes a bit of sense: Even in X/Y, they were using the box legendary as a power source, and there were some offhand comments about there not being "enough" to complete the plan.
Well, in Z, they get BOTH, and it's enough. So Zygarde must intervene, and Lysandre tries to stop it, since Zygarde is interfering with his plan.
What ensues is a double battle: You and Zygarde against Yveltal and Xerneas. And you have to capture one of them.