Here an explanation, straight from the civilopedia:
This is the special victory for Harmony. In this victory, the Harmony player triggers the merging of the consciousness of all living things with the latent sentience of the planet itself, resulting in a mass enlightenment and the end of all autonomous, individual identity. All beings are united in “planetary nirvana” to live forever in perfect harmony.
There are three steps to a Transcendence Victory: contacting the Planet’s Consciousness, creating the Mind Flower, and merging consciousness.
The first step for the Harmony player is to establish communication with the integrated consciousness of the planet. This is achieved by unlocking a series of technologies that lead to the Mind Flower wonder.
The Mind Flower is a Planetary Wonder unlocked by a late-game technology. It is buildable in any of the player’s cities.
Once a Mind Flower has been constructed, it will immediately begin a consciousness merge between the planet and the life forms that inhabit it. This takes some number of turns during which the indigenous life of the planet reacts to the process in dramatic, sometimes destructive ways.
The speed with which the Mind Flower can accomplish the victory can be enhanced by building Mind Stem and Xeno Sanctuary buildings in the player's cities. Each building built adds to the Mind Flower's completion rate.
As long as the player can protect the Mind Flower until the process is complete, the victory will be achieved.
If the Mind Flower is destroyed during the merging, the victory attempt fails. The player must construct another Mind Flower and restart the process to complete the victory