There are at least 4 known endings of this game depending on your choice on Mars.
Naturally Spoilers Abound
If you choose to join the Federation you'll get to the map cc_shadow, there you talk to some representatives of the Feds and follow Cyrius to cc_falling. Here you tell your mentor that Cyrus is a traitor and recieve the order to kill him. You'll travel with your mentor to cc_ancient.
Your mission is to find Akmal, who is hiding in one of the two large (flooded) tanks youll find at some time. Talk to the Looter next to it. He'll tell you how to drain the tank and mark both mission points an your radar.
You will be send to the temple (cc_severed) where your mentor awaits you. After a short talking, he'll initiate an attack on you. Kill him, talk to the drone and then kill the 4 pillars and Rimanah.
You'll be awarded with Triangular Gate.
Note: Another way to get this ending while skipping cc_falling altogether is to confront your Mentor on Mars and agree to help him instead of kill him. Doing so will bring you straight to cc_ancient.
On Mars, follow the Feds. Assist Cyrus in Coop (cc_falling) and talk/hack/kill the emissaries or plant the hacking devices. Next to the Exit you will find the Looter "Balthazar". He will award you with Substitution Gate if you don't affront him too much during the conversation.
You'll be sent to Temple (cc_point) with 6 very tough guards(Hack/kill the interceptor to keep them alive). Eliminate the 4 Pillars and Rimanah.
On Mars, do not join the Feds. Continue completing the given tasks and kill your Mentor behind the Ancient portal. Also talk to and fight the Werewolf at the bottom of the giant hole. You'll will be sent to eliminate the Jian (cc_purge). After that mission, when entering the Temple (cc_dreams) the werewolf "Amarok" will award you with Hypnotic Gate.
After recieving the third and last Gate Psi Power, finish the game in any way. In the Cave at Gamestart where you pick up the gun turn right. You'll find a large Portal. Step in.
In Minos (cc_minos) you'll find only 1 NPC willing to talk to you. You will be given a choice. Choosing to pass the Frontier sends you to The End (cc_end) while choosing to continue will begin the game again as will attempting to kill her with physical weapons.
Rumors say that there is no end, so that you have to quit the game by yourself. Others tried to destroy the seal (that Circe tells you not to) and continued with the circle. It's also possible to "kill" Circe with the Substitution Gate however this merely leaves you trapped in cc_minos with no way to progress beyond killing yourself. There are also several hackable Inferno objects however these appear to be unfinished mechanics that Streumon never removed.
The current True ending is not the original true ending according to a posted discussion with a Streum developer. The original ending was much more explanatory but ultimately changed to be more open ended allowing the player to color the story with their own experiences. Furthermore despite supposedly being in the game the ending was inaccessible due to absurdly high requirements(a greater than level 50 character, completion of all levels including side missions, 10s on Klaadums ladder for all missions as well as all 3 gates) as well as bugs that made achieving 10 on the ladder impossible on some levels.
RE: An official link to that discussion would be helpful for a large community of confused veteran players of E.Y.E.