I had a quick look at the episode in question to get some context. You'll see in the show that there is a small tree (a bonsai) at the front of the room and a boy is taking care of it. That is, he is tending to the tree. Apparently, this is a formal assignment and the child who is assigned to tend to the tree is called the "tender of the tree." This is not a common title in the real world - it's significant only in the world of the show and sounds somewhat formal and ritualistic to my ears.
The simple meaning of what the speaker is saying is that she remembers when the man she is talking to was a boy and he had the assignment of "tender of the tree" - that is, it was his job to take care of the small bonsai tree.
The deeper layer to what she is saying is that this position of "tender of the tree" is apparently a position of great trust and honor - bonsai trees are delicate and in the world of the show (which takes place on a space station after a catastrophe on Earth), plant life is rare and precious. But now as an adult, he is challenging the leader's authority during the time when the tree is being tended. She is implying that it is remarkable that a child who was once so trusted ("you were so cute") could grow up to be a rebel.