Sephiroth is capable of feeling empathy, and he’s even more capable of realizing when enough is enough. This is one of those moments. He’d aided in capturing you for Shinra one month ago, but you’re already unrecognizable to him. A once-proud ninja of the Wutai clan, reduced to a shell of their former self.
By the time Shinra starts to discuss plans to ship you off to Midgar, Sephiroth is fairly certain you won’t survive the journey. So he breaks you out. It’s an easy ‘malfunction’, and no one suspects him of being the culprit behind it. Ensuring your compliance is a different matter though; he is essentially the reason you were captured in the first place.
“Stay quiet if you want to live,” he intones quietly when you come to. The Wutai you knew had been brought to its knees, crippled by Shinra’s strength. Now, he wanted to see if you would rise up and help it rebuild.