During the attack by the "worst creatures in existence," he ordered Javic to flee with Gray, and, eventually, Franklin was killed by the creatures. Javic returned home to find his mother cradling Franklin's corpse.
Franklin later appeared to Javic, then going by "Jack Harkness", when he was hunting a Weevil in the sewers. The memory-changing alien Adam, masquerading as one of the Torchwood team, made Jack remember his past. Franklin was included in that illusion. (TV: Adam)