After learning of the (possible) location of Connor, a group of soldiers are sent on a mission, not to save him, but simply to find him. Up until now Connor’s only been a voice on the radio to these people, inspiring revolution, but also doubt. Most human colonies only know of him through story and myth.
Arnold is the leader of the group (some soldiers don’t want to be on a mission to save a myth). Kyle Reese is one of the soldiers (who looks up to Arnie as a father-figure), The other soldiers are a rag-tag, likable bunch. Their mission leads them across a scorched earth, surviving HKs along the way.
About a third of the way into the film, the group finally meets Connor (working out of the cave at the end of Part 3). He and Arnie square off, because Connor immediately thinks Arnie is an infiltrator unit (everyone else thinks Connor is crazy since those units don’t exist … yet). When Connor meets Kyle, he immediately knows his next mission: find the location of the time machine to send Reese back. In the meantime, father and son grow to know each other.
Their first mission is to a Skynet server or hub of some kind. The mission is to steal information (location of the time machine/defense grid). They succeed, but to survive they must survive a small army of Terminators. Connor and Kyle manage to escape, but notice that the robots weren’t trying to kill them, but capture them. The rest of the group is either killed or captured. Arnold is captured.
The information they stole reveals the location of the time machine outside of LA. As they prepare for their mission, we cut to Arnold’s character being taken into a facility where he is eventually used as one of the “skins” (literally) for this new infiltrator model.
Final sequence has Connor and the gang cutting loose the night before the mission. Reese wanders off for a moment to himself and the picture of Sarah Conner, when Arnold shows up. Just when they are about to cheer the return of their friend, he opens fire. (This is the scene from the first movie when Reese loses the picture). They barely survive the attack, but have now learned about the infiltrators.
For a year now, the Resistance has steadily worked toward infiltrating SkyNet’s defense grid/time machine. Connor struggles with either A) sending Reese back, or B) taking the chance that not sending him back might actually stop all this, even if it means Connor never exists. Reese is the proud right-hand-man to the legendary Connor, who is also his new father figure.
Connor gives Reese the order, sending him back through time, and then destroys the facility and smashes Skynet’s defense grid.
Film ends in a similar fashion as T2, with Connor now heading into a truly unknown future (as is the audience).
The war has not ended. Connor considers himself a failure. Thanks to the info gained in Part 5, The Resistance has developed a virus which can destroy all the machines. In secret, Connor has been fixing and reprogramming the Arnold-bot from the end of Part 6, in order to send it back through time, which for Connor, is the last hope he has for ending the war. A blood bath occurs in San Francisco, a human sanctuary, where a bunch of humans massacred each other. Connor learns of a virus the machines are preparing to unleash which is essentially like the “rage virus” from 28 Days Later.
Connor’s missions are a race against time as he tries to upload the human-developed virus into the machine’s network, and send the reprogrammed Arnold-bot back in time, before the machines can finish loading a plane which is going to crop-dust humans into self-inflicted genocide.
Connor succeeds, but not without sacrificing his own life.