Tentative outline for my next story:

4 parts, each with a different POV.

Part 1: 2019; John Connor's POV.
Kate Connor, as one of John's lieutenants in the Resistance, is charged with destroying a new SkyNet facility of which the Resistance has received information that it is the machines' first attempt at creating a working time-travel mechanism.
John has to remain behind at headquarters. He looks after his and Kate's twin babies, Sarah and Kyle, and ponders the strange attraction he feels for Marcus Wright.

Part 2: 2019/2032; Kate Connor's POV.
Kate's team is either killed or evacuates the building, while Kate is in its center and discovers that the plans have proceeded further than anticipated: SkyNet's mechanism is almost ready for its first trial. In immediate danger of being destroyed, SkyNet decides to risk it and send a T-800 model 101 Terminator through the mechanism to travel to the year of Sarah Connor's birth and kill either its mother shortly before delivery, or baby Sarah. Kate has no other choice than follow the Terminator if she wants to preserve the original timeline.

Part 3: 2032, future John Connor's POV.
Kate arrives at a SkyNet facility of the future, not, as thought, the past. So did the T-800. They fight, soon joined by future John Connor and possibly future Marcus Wright. John and Kate are both shot; John not lethally, while Kate gets shot in the gut. She knows there's no way the human's medical facilities will allow to heal her wound. They destroy the T-800's body, although its head is preserved. Kate extracts its CPU and re-programms it, planning to send it back to 2004 so it can help past-John Connor and herself evade the T-X. She asks John to put the re-programmed CPU into a current T-850 model 101 Terminator and send it back, using a closed-down SkyNet facility (John had it secured by pulling the time-travel mechanism's main component). Her program includes partially falsified information. By not telling her younger self of her death and announcing John to have died in 2032, she hopes to give their younger selves the strength and motivation to get together and fight the machines. She's comforted knowing that her children are alive and happy (and around 13 years old), and that John has found love again in Marcus.

Part 4: 2019, Marcus Wright's POV.
Marcus ponders the events of the last months (Kate has been declared KIA when the facility blew, although John mourns having no body to bury), wonders about the time paradox regarding 2032, but enjoys growing closer to Marcus.
They have both mourned their lost loves (Blair was given the lead of another Resistance cell in another country and left before things between the two of them could become physical beyond 2nd base).
Marcus thinks about his growing acceptance among the Resistance and John's family, John's attempts to stay close and yet distanced from Kyle Reese, and lives through his and John's first time of having sex.
Marcus can feel, although physical sensations are muted in his new body. The sex is rough, John uses his teeth and nails to stimulate Marcus' skin, Marcus has no prostate, so all sensation while he's on the receiving end have to come from his cock and balls, and his anal muscles. John admits to (and lives out) his Terminator fetish.

the end.

edit 07 Jul 2009: Realized - with slight changes - as "Missing In Action, Presumed Dead".