If you managed to get an alliance conquest ending (having a Pact of Brother/Sisterhood with all the remaining factions), the ending text reveals that the remains faction leaders were finally able to put their ideological differences aside and unite humanity to face the dangers of Planet as one. They're working along side each other as colleagues like they once did on the Unity.
Secret Projects like "The Dream Twister" show the horrific side of telepathy and psionics. But then, there is "The Telepathic Matrix", which shows a soft side of a woman in a beautiful garden, wind following around her. It's accompanied by a poem from Lady Deidre Skye, in which she compares warm thoughts to a blanket that warms the soul.
One might find the relationship Deirdre and Planet develop over time to be somewhat heartwarming, considering the fact that the introvert who spends most of her free time with plants is not only communicating with the planet itself, but almost developing a sisterly relationship with it.
Transcendence has humanity exploring the universe without spaceships, and after a few millennia, finally return to Earth and clean up the mess they made.