The Machine's Child by Kage Baker
Alec Checkerfield's piratical AI, Captain Morgan, has masterminded the rescue of Mendoza the botanist. It takes a lot to kill an immortal, and they tried hard to kill Mendoza, whose body is destroyed and whose memory has been nearly totally erased. She is grown a new body and raised to consciousness. The captain has also retrieved the personalities of her dead lovers, Nicholas and Edward, who are clones of Alec and now inhabit the same body as Alec, an uncomfortable symbiosis. Everyone's favourite immortal cyborg, Mendoza, and the three incarnations of her not-quite-human love, Nicholas/Bell-Fairfax/Alec are all together for the first time. And now they can really begin to fight back against The Company. The Machines Child is the one fans have been waiting for, the start of a complex and gripping war along the timelines.