Born on Earth in 2220, Stephen Franklin was the son of Richard 'Firestorm' Franklin - a third generation career soldier and a war hero. Because of this, young Stephen spent most of his childhood alone with his mother and his four sisters, Juanita, Maria, Celia and Cathy, hoping that father would return home alive. Still, when their father was home, the children were treated as if they were soldiers. After seeing his father being saved by an alien doctor, Franklin decided to pursue a career in medicine and eventually began studies in Harvard, specialising in xenobiology. Franklin's choice of career didn't please his father and after graduation Stephen left home to hitchhike around the galaxy.

When the Minbari War began, Franklin returned to Earth and joined EarthForce. He wanted to help in the defence of his planet, but he wasn't about to go as far as to turn over to the bio-weapons division the notes he had made on Minbari physiology during his hitch-hiking years. Franklin destroyed the notes and was imprisoned because of it. He was, however, never officially charged of anything - probably partly because of his father. Franklin was eventually released, but only after agreeing to join John Sheridan and G'Kar as a representative of earth in secret peace negotiations. The negotiations failed and had Delenn not granted the men amnesty, they would have been executed by the Minbari.

Franklin arrived on Babylon 5 in 2258 when Doctor Benjamin Kyle, the head of the station's medical facilities, was recalled back to Earth. During the next few years Franklin continued to get into trouble by standing up for his principles. For example, when alien parents forbade him to perform a vital surgery on their son, he operated the boy without their consent. Besides his main job Franklin also worked on a free clinic in Down Below and led an underground railroad for rogue telepaths.

All this work combined with his perfectionism and the increasing problems the station was having with both aliens and Earth, led Franklin into an addiction to a legal stimulant known as stims. He was quite a religious man (follower of a faith called Foundationism) and after acknowledging his problem he decided to leave his job and begin a walkabout to rediscover himself. The stim withdrawal symptoms weren't Franklin's only problem: he fell in love with a woman called Cailyn in one of Down Below's bars only to find out that she was terminally ill. The walkabout almost ended badly when Franklin some time after this was mugged and left to die. While bleeding to death he had the revelation he had hoped to find on the walkabout and this gave him enough strength to get help. After recovering Franklin was pleased to find out that Sheridan wanted him to resume his position as the chief medical officer.

In mid-2260, some time after the Shadow War had come to an end, Sheridan sent Franklin and Marcus Cole to Mars to meet with the leaders of the other resistance groups. Despite of Marcus' continuos attempts to drive him insane Franklin was eventually able to talk the resistance leaders to join their cause. It was during this visit that Franklin also had an affair with Theresa Halloran, the leader of the Mars Resistance. Their relationship cooled down a bit when Franklin some time later returned to Mars with Lyta Alexander and the shadow-enhanced, cryogenically frozen telepaths.

When Michael Garibaldi, brainwashed by Bester, betrayed Sheridan and then tried to prove his innocence by contacting the resistance, Franklin was the only one who gave the ex-chief of security the benefit of the doubt and thus saved his life. Lyta backed Garibaldi's story with a telepathic scan and the three set out to rescue the Captain from President Clark's forces. The rescue mission succeeded as did Sheridan's plan to use the shadow-telepaths to disable the enemy ships. Unfortunately Franklin's next mission didn't. As soon as the fighting ceased, Franklin took one of the whitestars and tried to get back to B5 in time to prevent Marcus from using the lethal Alien Healing Machine. By the time he reached the station, the Ranger was already dead.

Some time after the founding of the Interstellar Alliance, Delenn and G'Kar came to Franklin and asked him to begin research on possible cross-species infections. Franklin delegated some of his work as the chief medical officer to his underlings and accepted the job.

In late 2262 Franklin left behind both B5 and Halloran (who had just been appointed as the head of covert intelligence for the Alliance and had thus moved to B5) when he was offered a better chance to pursue his research on cross-species infections. Kyle, who after returning to Earth had been acting as the chief of Earth's xenobiological research division, was now retiring and wanted Franklin as his successor.

Four years later, when the Drakh infected Earth with their biogenetic plague, Franklin was on Earth and led the fight against the plague from there. Still, he had the privilege to leave Earth at least once during the epidemic when he in 2267 visited the Excalibur in order to help Doctor Chambers conduct an experiment where a healthy volunteer was infected with the plague.

Franklin survived the epidemic and was still working in the xenobiological research division in 2281.