Blitzcriegpop explains, shortly, how to get gear.
Truth is, it's a bit more complicated this patch. There are a couple of articles that try to explain it a bit, you can find them on the main page, under "Announcements" News, or on the Guild Portal, where there is an
article that contains all the links to post that explain different features of the new patch.
To give you a direct answer to your question: There is only one way to get green lvl 65 base items, and that's from the npc near the upgrade anvil in the academy. The cost might seem a lot, but considering how easy it is to get gold now, i think it's just a moderate price to pay. Not cheap, but not that expensive.
As Blitzcriegpop pointed out, you can get Rare (blue) reputation gear in the main Ferris Camp (forgot the name of the map) and that gear will let you do S1 at least.
You can also get crafted epics, which are way better than reputation blues, but also cost a lot more than lvl 65 base greens, unless you craft them yourself.
Also, welcome back to the game
Your name seems familiar, so we might have met before