Just some pretty obvious hints to Jefferson that were in previous episodes.
Episode 1:
Jefferson says "I could frame any one of you in a dark corner."
A possible hint to him "framing" Nathan from most of his antics for EP4. All throughout EP4, we assume Nathan and his family are the only ones involved in the dark room. Yes, Nathan is most likely involved in Jefferson's "ring", but as I said, throughout most of EP4, it heavily implied Nathan did it all.
His photographs around campus
If anyone checked the photos around campus in EP1, most of Jefferson's photos are of young girls, in "vulnerable" positions.
What do we see in the dark room in EP4? Pictures of Kate and Rachel, in vulnerable positions, tied up, among a load of other girls.
Episode 2:
Kate mentions hearing a soft voice while she was out of it
Nathan doesn't have a soft voice. At all. He's really quick to be loud.
Mr. Jefferson, on the other hand, tends to be really soft spoken all of the time.
Even when being "told off" by Principal Wells in EP2/3/4, he remains calm.
Unlike David, who is quick to retaliate, calling Max a punk and Nathan threatening a lawsuit.
Mr Jefferson gets a tad defensive when Max brings up Rachel Amber
When talking to Jefferson in EP2, after Kate walks out, Max has the option to say "I don't want Kate to become the next Rachel Amber", to which Jefferson quickly says (and in a slightly different tone than is usual tone) "Rachel Amber? What has she got to do with Kate?"
And of course, the "Maybe she means well, but doth protest too much" remark.
Episode 2/3:
Hanging out with his female students after hours [Possible citation needed]
If you choose to blame Jefferson in EP2, Pr Wells will say "Mark, I know Miss Marsh has assisted you in class", implying Kate may have stayed behind to help Mr Jefferson clean up after class/help prepare the lesson, which seems like something she would do, so most people may have overlooked this.
In EP3, late at night, he's seen exiting the school with Victoria. For reasons unknown. Could Victoria be trying to get on Jefferson's "good side" or something else?
Episode 3/4:
Nathan being "out of it" in Rachel's picture
I didn't noticed it too much at the beginning, but after replaying, have a look at Rachel's photos.
In her "buried" pic, there's a boy, who also appears to be knocked out of it too, next to her body.
I think this boy may be Nathan, as the boy has similar clothes/hairstyle to him.
If it IS Nathan, then who took the picture?
Episode 4:
Whiskey in the dark room
If you search the dark room, you'll find some whiskey infront of a sofa.
Only 2 people have been shown to have drunk whiskey: Principal Wells and Mr. Jefferson (EP1 ending)
Nathan hasn't been shown to drink whiskey at all. Nor has anyone at his Vortex Club parties.
How did "Nathan" know Rachel's body was found?
Max and Chloe told NO ONE about Rachel's body. Not Frank, not the Police and certainly not Nathan.
They wanted to get Nathan, but he was nowhere to be found. At all, he wasn't at the Vortex Club party.
Disclaimer: I am in NO way saying Nathan is 100% innocent.
So yeah, some hints from previous episodes I managed to pick up.
What do you think?