The natural sciences WERE the subject of our discussion.
There's some nuance here. Let me walk you through this.
This isn't quite as unambiguous as others here have mentioned. Here's why:
This is correct -
[NOUNS] were (< plural verb) the subject of our
discussion.
So it seems clear that the correct form is 'natural sciences were the subject of our discussion.'
However, 'natural sciences' may not refer to something that is plural. Instead, it may be the name of something that is singular and implicit in the sentence, a college class for instance.
Contrast this correct statement (about a class) with a singular verb:
Natural sciences starts at 9 AM.
With the plural verb:
Natural sciences start with nature!
If you had asked,
Natural sciences WERE the subject of our discussion.
or
Natural sciences WAS the subject of our discussion.
The correct answer would have depended entirely upon context.
There's another nuance here though. It's uncommon to include 'the' as part of something's name in English, and supports the idea that you're speaking of actual natural sciences (plural), and not a class.
Because of that, the correct form here is -
The natural sciences WERE the subject of our discussion.