A majority of us here are sad that Rachel died, that's obvious. I think it was a bit much, and she should've seen the end. But, thanks to modern fanfic technology, she doesn't have to stay dead! So let's post our theories and try to find the most logical.
My pick is this: The one was a kind of entity on the Blade Ship, right? and this is where Rachel died, remember. I tihnk the one was a kind of parasite, another offshoot of the yeerks if you will. He's been hiding out in the shadows, waiting for his moment. He finds rachel and, on pure instict, aborbs her mind into his. This gives him sentience, and he goes on a wild road tip through the universe findign toher suitable hosts, untill he's found by Ax & company. <Witty Borg reference here>. Anyways, assuming those on board the Rachel don't get blown up, Tobias manages to get through the One's...evilness, and contacts Rachel, who's in there with Ax. They're able to get out while the One is momentarily disabled, but since only Rachel's mind as cosnumed, she would be gone as soon as she freed herself. So Ax sacrifices his body, stating that she deserves it more than he does. She manages to split off from the One, and is alive. Yay.
(I'd like to say this right now. Some of you will say that Rachel needed to die, despite the large amounts of suck. And some of you think she should stay dead. Well, this isn't the thread for that. Go vent somehwere else. This is for people who miss her and regret her death, and...well, want to see how far the fabric of the Aniverse can stretch to bring her back.)