They were able to exist outside of time and space simultaneously, and be one with space and time. They travelled across the universe using roads, called Phaeron Roads, which were said to be made from space and time itself.
By the time that the Twelfth Doctor and Clara Oswald joined the crew onboard the Alexandria, the Phaeron had disappeared from the universe for over a million years. Their disappearance was originally unknown to the universe. However, as the crew of the Alexandria found out, they had discovered the Glamour and it ruined them, so they closed off all the roads, created one last wormhole to dispose of it alongside themselves, when the Carthage flew straight through it, trapping it and the Phaeron, whilst the Glamour remained in N-Space. The Phaeron eventually all died out, leaving a holographic message onboard the Carthage for anyone who might find it. (PROSE: Deep Time)