I don't now if there ever was such a scene, but I remember this one scene in the and of #32 when Rachel is whole again and he said to her: "<Yeah. Let's go, Rachel,> he said. <The two of you and the two of me.
Let's go.>"
I think this shows how he loved her the way she was even if she had this two sides inside her.
And yes in the final arc she was all alone because except Jake nobody knew what she would do. So there was no one to help her.
A bit off topic, but I loved the scene when Tobias learned what Jake did and when he understood Rachel would die. This sowed how much he loved her.