I am not sure if they cut the scene or what but some part is missing:
What happen after arnold found out t3000 who disguise as a fbi lady and fought with him? The next scene of arnie show up getting up the chopper and suddenly t3000 has a assault rifle, some scene is missing.
The scene on how t3000 get a new chopper were also omitted.
The police station scenes are somewhat messy and nowhere as good as the original police station scene from T1. The sequence of events if I recall is something like this:
SPOILERS
Arnold shoots T3000, saves the detective and chases after T3000.
Detective frees Sarah Connor, Sarah passes by young Kyle & then gives him the "straight line don't look back" pep talk before escorting young Kyle & his parents to safety.
Meanwhile I think it is Arnold who gets adult Kyle. (This part is where I seriously can't recall, I find too chaotic and not memorable at all)
Anyway they regroup in the police armory where the detective returns them their bag of C4 charges and leads them up to the helipad after they rearm.
T3000 reaches the roof just as Arnold, Kyle & Sarah are boarding. Arnold retaliates while Kyle pilots them away to safety. This is where T3000 is shooting them with a rifle.
Since there are 2 helicopters, T3000 pilots the remaining one and chases after Arnold, Kyle & Sarah.
T3000 did not get a new chopper. His chopper crashed after Arnold takes it out but by then they are all at Cyberdyne HQ already. It is logically assumed that T3000 simply swims ashore and reaches the office before anyone else. If you recall the chopper crashes right at the helipad of Cyberdyne.
