The Face of Boe has supposedly lived for billions of years, watching as the universe has grown old. A wise and compassionate being, he also knew many of the great secrets of the cosmos, including one that he would impart to the Doctor at the time of his death.
The Face of Boe first appeared in the episode "The End of the World" as a guest aboard Platform One in the year 5.5/Apple/26, attending the "Earth Death" event. He did not speak on-screen during this episode.
In the episode "New Earth", 23 years after Earth Death, the Doctor and Rose Tyler visited the hospital in New New York where the Sisters of Plenitude were caring for the Face of Boe, who was apparently dying. The Face had sent a psychic message to the Doctor and his carer, Novice Hame, told the Doctor that the Face of Boe would impart his greatest secret upon his death, but only to one like himself: an ancient traveller of the stars, a "lonely god" as Hame put it. However, the Face would recover from his ailment and told the Doctor that the Time Lord had helped him to see the universe in a new light. He then teleported away to an unknown location, stating that he and the Doctor would meet again one last time.
In the episode "Gridlock", 25 years after the events of "New Earth", the Face of Boe was nearing the end of his life. Following a horrific viral outbreak that wiped out New Earth's surface population, the Face and Novice Hame were left alone within the ruins of New New York while the denizens of the Undercity were trapped beneath. Sensing the Doctor's arrival, the Face sent Hame into the Undercity to find him. After Hame brought the Doctor to the New New York Senate Hall, they attempted to open the skygates to the Undercity and let the citizens ascend and repopulate the Overcity. In order to provide enough power to the skygate, the Face of Boe used his remaining life force, shattering his tank and exhausting his smoke.
As the Face of Boe lay dying, the Doctor urged him to try and carry on. The Face responded that the Doctor knew better than anyone that all living things have their time, and imparted his final secret to the Doctor: "You are not alone." The Face of Boe then died.
The Doctor speculated that the Face of Boe's last words might have been in regards to the Time Lords who had all supposedly perished during their war with the Daleks. The Doctor dismissed the Face of Boe as being mistaken, but in the episode "Utopia", he would discover that another Time Lord had indeed survived the Time War. However, that Time Lord would turn out to be the Doctor's arch-nemesis, The Master.
In the episode "Last of the Time Lords", Jack Harkness commented on the fact that when he was younger on the Boeshane Peninsula, the first person there to join the Time Agency, he was nicknamed the Face of Boe. This led the Doctor and Martha to speculate that Jack may in fact be destined to become the Face of Boe himself.