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The Special Edition runs about 16 minutes longer. Among the new/alternate scenes:
-The orderlies are shown forcing Sarah to take her medication.
-Sarah has a long nightmare, involving a visit from Kyle Reese in the hospital leading to a playground/bomb scene outside; this dream happens just before she is seen describing it on tape.
-The T-1000 steals a police car after John and the T-800 get away after the canal chase.
-The T-1000 realizes the dog is not named Wolfy and kills him, after the phone call from John.
-Instead of simply stating that the T-800 learns from humans, there is a long scene in the garage where John and Sarah open him up to change his processor from read-only to learning; Sarah almost smashes the chip to end it all but John talks her out of it.
-John tries to teach the T-800 to smile at the gas/food stop.
-Dyson is seen at home working on the Skynet chip prototype. His wife comes in and reminds him he's promised to take the kids to Raging Waters. Dyson explains to his wife what a neural net processor is and how it will change mankind for the better. (This happens after Sarah asks about Dyson in the first place.)
-At Enrique's house, John and the T-800 are stacking up ammunition. They start to talk about emotions and fear of death. John describes his childhood and his feelings about his mother's previous lovers.
-As John and the T-800 race after Sarah to prevent her from killing Dyson, John explains to him that killing is always wrong and life is important. At Dyson's home at night, a series of restored and rearranged shots show Sarah assembling her weapons (with an alternate line from Tarissa), thus building the tension of her stalking Dyson outside in his backyard.
-At Cyberdyne, the gang destroys the lab; Dyson himself shatters a large scale model of the Skynet chip with an axe. There is a dialogue change as the police arrive, since the police radio dispatch is not continuous anymore. The theatrical edition mentions the 1984 police station shootout, and the special edition focuses more on a repeat/correction of the Cyberdyne address.
-In the factory after the T-1000 is shattered, we see that it's beginning to lose control of its morphing. Its hand takes on black and yellow stripes when it grabs a railing, and later its feet squish and morph into the steel floor pattern on each step. Several minutes later, when it morphs into Sarah Connor, John looks down and notices the T-1000's feet combining with the steel floor right before telling the real Sarah to shoot it.
-After the theatrical credits have run in their entirety, there are special edition credits.
-Alternate ending - Following the T-101's demise we cut to many years later we see an elderly Sarah sitting at a park watching an adult John playing with his daughter. Sarah mentions Judgment Day didn't happen and John became an American senator. After Sarah ties up her granddaughter's shoe laces, Sarah then mentions the T-101 and that the T-101 could learn about the value of human life and hopes someday everyone will do too and the film ends.
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