- last post: 01.01.0001 12:00 AM PDT
If you read "First Strike", there are hints in the book that show that whatever Dr. Halsley and Kelly are up to, it is related to the crystal they found in the underground facility on Reach. In one part of the book, Dr. Halsley converses with Cortana about the crystal and discovers that the artifact bends not only space, but time as well, which explains the anomaly in the dates the events took place. Dr. Halsley must know this is important to the preservation of the human race, so she erases Cortana's memory of the conversation regarding the artifact.
Dr. Halsley's mission with Kelly seems to be important because she states that once she starts with the "mission", there would be no turning back. She also refers to the fact that she will do anything in her power to save every human being, instead of sacrificing the few to preserve the whole human race, which is evident because of her guilt towards the creation of the SPARTAN 2/MJOLNIR project. I have no idea how this relates to her kidnapping Kelly, though.
Also, at the end of the book, Tartarus(sp?), a Brute, speaks with a Prophet about their plans to destroy the human race. At one point, Tartarus shows the Prophet the glass shards of the alien artifact that bent space and time. Though destroyed by Corporal Locklear, the artifact still had the capability to distort gravity. Also, the Prophet tells Tartarus that the remaining pieces of glass may be enough to serve their initial purpose, which is why the Covenant didn't completely glass reach when they obviously won the battle. This is probably what Dr. Halsley and Kelly are up to: To find the rest of the crystals and destroy them before the Covenant gains control over them. Either that, or they went to some secluded planet to retrieve the Mark VI armor.
Your guess is as good as mine, just shedding some light on information on the books leading up to Halo 2. If i missed something, or there is more interesting information, please, post it.