Only real hidden endings are to not help in the last mission. It becomes another sector like Presidents End.

The game is less about the story. Some would say the journey is more fun than the destination. Other things you can do: genecide, declare war on a race and eradicate it from the universe. Replace all of the NPC stations with your own one by one. Create a huge empire with 300 factories and service transports plus protection/patrol ships. Restart and play another way.

theres a hidden gate in dukes vision or round there havent explored it though