The third act was mostly changed due to Helena Carter. The scene was somewhat rushed design-wise and they knew they might have to reshoot it right after they shot it.
Said to be to hokey or Star Trek-esque, they needed something simpler because time was running out. All they knew is that it had to be changed.

The original scene consisted of Marcus sneaking into skynet like you see in the movie. He then hides in an old church as it gets bulldozed by a giant Terminator (as seen in the preview). He hides from some T-600s and looks up at the skynet building. He sees a light on the 5th floor and sneaks in. When he walks into the room a Male Hybrid is at the computer system typing away. He notices Marcus and gives him a warm greeting. Marcus looks at him and then throws him out of a window. The hybrids neck snaps and Marcus then uses the computer console.
Meanwhile Connor Sneaks into Skynet and kills a T-600 by destroying an elevator shaft.
There is a different scene in which Kyle is kidnapped and taken up to Serena.
Marcus has a conversation with Serena much like the one in the movie except she is a Hybrid. She also has a pet T-800 that puts Marcus in the chair. After she tells MArcus of her plans there is an alternate scene of Ashdown getting destroyed in the sub.
Marcus escapes the T-800 and grabs Serena, ripping out her chip. The robotic arm in the room mistakes her for human and rips her apart.
As Kyle escapes with Connor and Star they blow away the wall, but the other side of the wall is not actually the Terminator factory, its the prisoner cells. There is a scene where Connor saves all the prisoners and they escape. He gets chased by the T-800 with the mini-gun from the T-600 and THEN they jump down a silo into the Termiantor Factory.

A lot was cut out of the end. There was also a long dialogue sequence before John leaves. He talks with Kate about how much they love each other and of their unborn child.

Also, At the end, Barnes has more of a role. He helps rescue Marcus and Connor and then is responsible for getting all of the prisoners to safety. Blair has trouble with the helicopter and Marcus saves the day again.