Once it became apparent that they would not be abandoning the senior Legionnaires and their mission (the true mission of the Legion), Zenyatta complies with what the mysterious voice asks of them. There is a moment of internal alarm when they are placed in a secure room, but the explanation placates him.

"Your apology is accepted," Zenyatta replies earnestly, though such a reply is probably unneeded. "A number of questions about our security detail changes come into a different light with what you have said. I assume the AI are also responsible for our long range communication difficulties."

Kid Quantum was supposed to have the ability to contact the Legionnaires not on this mission, but if she's compromised then, then they have no communications. And they weren't the only junior group placed on security detail. "Do you know what has happened to the others on our team?"