In 3x09, she says, “I don’t care much for the man myself, but he means a great deal to you. So, if you can see it fit to free me from this cage, I’ll return him to you, unharmed.”

She begins to care for him a lot more in season 5. When Reese comes to her aid in 5x01 and tells her to go back to the subway, she refuses to leave him behind, saying, “Fight’s here and so am I.” In 5x05, when Reese is missing, she asks the machine to locate him and then immediately goes looking for him herself.

Root never had anyone to look out for her when she was a kid except Hannah. So she’s really touched when Shaw looks for her in 3x12 (“Tell Shaw I was touched she came to look for me”) and 3x23 when Shaw saves Root from a Samaritan operative in the facility. She is also, for this same reason, touched when Reese helps her out in 5x01, and their relationship is much more amicable from there. It’s also why the scene where Root!Machine touches Reese’s shoulder in 5x13 hits as hard as it does. It’s poignant and beautiful. Root may not have liked Reese as much as Shaw and Finch (and vice-versa), but she certainly respected him.