the time war - the rise of gallifrey?

what did the face of boe (aka captain jack) mean when he prophesied, 'you are not alone'? was he refering to the survival of the master or is the answer more complex. in the eighth doctor novels a long running plot arc may offer the current production team some ideas. here is an extract from wikipedia.
Just prior to destroying Gallifrey, the Doctor (with Compassion's help) downloaded the contents of the Gallifreyan Matrix — the massive computer network containing the mental traces of every Time Lord living and dead — into his brain, with his own memories suppressed to make room for the data. Gallifrey had not actually been erased from history, but an event horizon in relative time prevented anyone from Gallifrey's past to travel beyond Gallifrey's destruction, and vice versa. Both the planet and the Time Lords can be restored, along with the Doctor's memory, if a sufficiently sophisticated computer could be found to reconstruct them. Before that can be done, however, there is the problem of the Vore to contend with.
At novel's end, the Doctor, Trix and Fitz are set to confront the Vore invasion force. The restoration of Gallifrey, in time for its second destruction in the
Time War prior to the events of the 2005 series has yet to be chronicled.