Case history:

I did not want to spend a lifetime tackling the graft-vs.-host problems associated with a Bone Marrow Transplant if I didn't have to.
I also did not want to have the possiblity of a relapse 10 years down the line. The high dose Cyclophosphamide did not appear to cause either of these.

The disadvantages of the Cyclophosphamide were the long, slow, vulnerable recovery period with low white counts, and the small but real chance of a fatal reaction to the chemotherapy.
I chose the cyclophosphamide.

The Cyclophosphamide's job, as I understand it, is to kill off the white blood cells, as they are malfunctioning, and let new ones grow from the stem cells, which Cyclophosphamide does not damage.
Kind of a chemical "rebooting" of the blood.