What Does The Ending Of Ex Machina Really Mean?
What Was Nathan Going To Do To Ava?
The second act sees Caleb, and the audience, presented with two versions of events; Ava says Nathan is lying with some ulterior motives, while Nathan insists he's engineered events so Ava will try and take advantage of Caleb. Now there's no debate here - it's Nathan who's telling the truth. There is ambiguity throughout the film to his real motives, but when Ava forsakes Caleb to escape on her own it's apparent she was merely using him to escape.
But what exactly was Nathan going to do with Ava after the test? At one point he muses about rewriting her code for the next update, but that's more to push Caleb towards helping her than a statement of intent. Assuming the sessions are looking for confirmation that Ava can think, the film is essentially a Beta test - ironing out any kinks ahead of moving forward with production - suggesting she's for the scrap heap once the whole thing's over.
That's shows a high lack of emotion - he's proving something can think just so he can destroy it - which probes further into Nathan's psychology.
Why Was Nathan Doing This?
Because he's a rather brutish character with a condescending tone, it's easy to think of Nathan as the movie's villain. And while he's certainly an unlikeable person, that's not totally the case; once it's revealed the sessions are just part of bigger experiment, a lot of his more genuinely questionable moments become mere mind games.
So what exactly was the genius up to? He's developing A.I., but for what purpose? His assistant, Kyoko (more on her later), proves he's developed a serviceable, if not perfect, form of robot help, but his aims go beyond just improving everyday life - Ava is less the work of a businessman, but of a scientist. And yet Nathan has corporate level secrecy, betraying unbridled passion as the real purpose behind her development.
The manner with which he rewrites recent conversations to be more epic, and keeps obsessing over Caleb's quoting of iconic phrases reveals a more self-involved motivation; he's perfecting A.I. to create his own legacy. Sure, he's aware of the scientific implications, but really only cares about "You're a God" being on a cultural plane with "Now, I am become Death, the destroyer of worlds." Which gives the whole 'creator killed by his creation' third act development an added sheen of irony - it really is bringing him down to Earth.