Well from the multiple responses and theories, plus my own experience in the game, it seems as if she is neither here or there. She has this "Enemy of my enemy is my friend" vibe going for her. When you first see her when you get the ship, it is possible she gave it to you. When you see her again on the moon, while looking for the missing guardian, she randomly appears then your character looks away then looks back and she's gone. Which means she is either assessing you or in some way guiding you, or both. When she finally appears to you on Venus, for me as an exo warlock, she was also exo, but hunter. She kept calling my Ghost a "little light" and even admits that she is NOT of the light, explaining why she has no ghost and looks like a hunter with a Fallen weapon and can teleport like the Vex. During the entire interaction she is talking to someone on a com-link about you and about some kind of battle then teleports.
I am just now on Mars and can't wait to see what unfolds but not getting my hopes up. This could be the beginning of the beginning lol.
Anyone who has played the entire story mission out knows there is more to it, given that Bungie won't charge for them since they are already on the game disc and is therefore illegal. Hopefully there will be more answers to the questions.
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Your response got me thinking what if she killed the guardian on the moon so she could see how we can handle the hive and that is why the ghost is not by the guardian. I think that she placed the ghost inside the temple