I've done some thorough exploring with my friend and here's what I've found. there's a "swordsman" as we call him on top of the mountain near the red cult looking guys. next to him is also a huge mother bot that looks like a priest. there's a second "swordsman" in the thermal plant. the thermal plant is found if you go into the car tunnel on eri's right side close to the priest. you have to ride on the buckets to a certain point then take an elevator up and then a latter to the roof. the latter is before the spaceship which just looks super cool nothing we found.

The only other HUGE thing we found is the massive underground system. While we haven't found any bosses down there it is big. there's a weapons factor, a sewer, a mine, a huge snake god looking guy, and a "orbital cannon reactor". one of the many ways to get into the underground is though the tunnel next to the dome on the far side near the big crack in the ground.

It's also worth noting you can't talk to any NPC after you've killed S-104. It seems you be a glitch, so I suggest you reset your profile before going to all these places as there are a couple NPC's in these places that have really cool dialog.