She does not believe in what her brother is doing. She, herself, once held one of the three legendary god cards. In the hopes that he'd help her stop Malik, Isis gave her god card - God Of Obelisk - to Kaiba. She also understands some of the history of the millennium items and is the first to tell Yami Yugi of the existence of his past memories.
Isis is also a top duelist and shouldn't be taken very lightly. She's one of the most powerful female characters in the series. However, there's a lingering darkness around her. She worries for her brother and of the future she sees.
During her battle with Kaiba, Kaiba sees a vision and is able to change the course of the future that Isis originally predicted. Kaiba gives her a sense of hope, and the pessimistic view that her visions gave her seems to fade. Noticing this, she gives her millennium item to Yugi. But now that the future has changed, anything can happen....
All she knows is that she must save her brother.