1999. Sarah Connor, in a waitress uniform, grabs future messiah John Connor out of his high school library. They try to run but the cops are waiting outside, and Sarah and John get stuffed into separate cruisers. When Sarah sees the Terminator approaching, she kickassedly subdues the cop who's supposed to be watching her. As the cops engage the Terminator (much to their detriment), Sarah drags John out of the cruiser and tells him to run for it. He does; the Terminator shoots him down; Sarah screams and begs for her own death; the Terminapocalypse happens around them; and Sarah wakes up from her nightmare, gasping. Her fiance, Charley Dixon, comforts her, not seeing the look in her eyes.
When John rolls out of bed, his mom tells him that they have to take off, fiance notwithstanding. John whinges: he likes it here, he likes Charley, no one knows them, it's been two years, it's safe. Sarah snaps: Don't you ever think that - no one is ever safe. We leave in half an hour: you get one bag and I'll go make pancakes. After the pancakes, they rabbit. Later, when Charley goes to the cops about his missing fiancee, hot FBI agent Ellison is there to bring him up to speed on the T2 events: mental hospital, high body count, blowing up Cyberdyne and Miles Dyson, etc. When Ellison updates the FBI/police database with Sarah's current aliases, a Terminator picks up the information.
Some time later, in whatever rural NM area the Connors have landed, a cute girl - "Cameron" - tries to chat with John at school, but he's uncomfortable with the attention. That night, he bitches to his mom about how his clothes are all wrong for this "hick town." Meanwhile, Ellison has tracked the Connors down because Sarah forgets to change her alias.
The next day, there's a new teacher in John's class: Cromarty. He's a Terminator, of course, and soon opens fire at John in the classroom, taking out poor cute Cameron while John dives out the window. John runs; Cromarty follows. At work at a diner, Sarah catches the breaking news on t.v. - shots fired at the high school - and takes off. In the school parking lot, Cromarty has John in his sights when a pickup truck runs him over. Cameron is driving. "Come with me if you want to live," quoth she, because she too is a Terminator, one of the good ones. John gets in the truck and they drive away. When Sarah scopes out the school, Cromarty grabs her. He takes her cell and uses her voice when John calls. At their house, Cromarty lies in wait, Sarah helpless beside him. A sweatshirted figure opens the door and speaks in John's voice. Cromarty shoots but it's Cameron. There's a hugenormous fight between these two Terminators, the great big guy and the tiny girl. John and Sarah get the hell out of there and Cameron manages to knock Cromarty out for a couple of minutes by hitting him with a bunch of electricity. The next day, Ellison checks out the wrecked house. Where's the blood?
John and Sarah are frustrated that this is happening again to them - didn't they take care of this during T2? No, says Cameron, someone else built SkyNet but she doesn't know who. John starts whingeing again (third time in one episode!) about how he doesn't want to be humanity's savior and can't his mom do something about it now so he doesn't have to? Okay, says Sarah, we'll find SkyNet and shut it down once and for all. The three of them go to the Dyson residence where Miles's widow is understandably reluctant to let them in. Sarah tells her that she didn't kill Miles - he was a hero - but is there anyone who was interested in his work? Theresa Dyson says no, no one (is this a totally useless scene or what?), then Cameron pipes up that they have to go now. Cromarty shows up; Sarah, John and Cameron commandeer the Dyson SUV and get away, but Sarah gets shot in the process. As Cromarty runs past their abandoned pickup truck, Cameron triggers a remote charge, blowing it all to bits. Cromarty is still coming after them, but he's looking a little rough now. The three find a hideout and Cameron stitches Sarah up.
In the morning, they go to a bank where Cameron waves a gun around and insists that the teller lock the three of them in the safe deposit box vault. Once inside, they open a bunch of boxes (which accounts she opened in 1963 and which subsequent time-travelers have stocked) and start assembling a sort-of nuclear weapon. Cameron opens another box which reveals a computer: it's an escape hatch/time machine and she can take the three of them out of here and into the future where they can continue their search for SkyNet. Outside, Cromarty has arrived and, completely disregarding the gathered cops, stomps inside and begins to systematically dismantle the vault door. Cameron sets the time machine to 2007 and just before they disappear from this when, Sarah shoots Cromarty with the sort-of nuclear gun and blows him all to bits.
2007: In a flash of light, Sarah, John and Cameron appear in the middle of a road, naked since nothing can come through with you on the time traveling. Cameron easily gets a carload of frat boys to pull over for her, then beats them all unconscious and takes their clothes. Now that they're in this when, 2007, no one knows the Connors are here and no one should be looking for them. Except that there's cellphone footage of naked Sarah being played across the television new broadcasts and both Charley (now married) and FBI agent Ellison see it.