It doesn't need to be a reboot. Just continue on with the current storyline. The machines keep their deal with Neo. Humanity grows outside of the Matrix and s

It doesn't need to be a reboot. Just continue on with the current storyline. The machines keep their deal with Neo. Humanity grows outside of the Matrix and starts thriving again. Freeborn humans become disillusioned with society start to break into the Matrix, while machines start sneaking out in human bodies. The machines and humans in power want to stop both things from happening and attempt to curb it in their own ways, which may or may not cause a new war between humans and machines.