Bingowings said:

Ilia was killed and replaced with a robot, a robot so well made that Ilia came back out of the robot.

She's inside the 'probe' of the 'intruder'.

I've been reading a lot of Rudy Rucker recently and this is exactly the sort of casual mindfunge he throws into his work.

The end of the film is essentially a three way bonking scene.

Decker, Ilia and V'ger getting it on and giving birth to God.

Kirk entering his ship is another such sex scene by proxy and the Enterprise orbiting and entering the V'ger vessel is a sex scene by double proxy with a lot of foreplay.

It's much more naughty than having Carol Marcus reveal her pants to camera for no explicable reason.

Not to mention Spock's little trip through the V'Ger "orifice".

I am never going to look at this movie quite the same way again.