I just realized tonight that the probable reason for Command (calling it Command since I'm still not sure what the two orgs are) to send Yoru in with Phoenix was to make sure Phoenix didn't screw up again. Why do I say that?

1. In the first cinematic he was overconfident and not only died as a result of it but also potentially allowed other people to die due to his failure to stop the plant. Also, when you consider that every mission for him is potentially zero risk due to his ability to reincarnate, you start to realize that he may be a bit careless when it comes to the goal of his mission.
2. He already faced Jett once and died at her hands, so if Command knew that there was a chance that she would be there again, they figured they'd send a second agent who was better equipped to handle her abilities.
3. Unlike Phoenix, Yoru can technically "die die". When you consider that, it makes sense that Yoru would have more motivation to complete the mission without being seen or even getting shot at. So he would therefore take more care around the enemy.
4. Yoru literally did 3/4th's of the work. He took out Cypher to cover Phoenix's ass. He outplayed Jett and pulled an Uno Reverse on her for what she did to Phoenix. He defused the spike WHILE IT WAS APPROACHING CRITICAL MASS. And THEN he took out Jett lol.

Someone said on one of my other posts that Yoru is basically Sasuke and Phoenix is Naruto. And I see it, as of right now, Yoru is basically Phoenix's handler and cleaning up his mess haha.