Dr. Franklin is a strong-willed, kind person and idealistic leader on Babylon 5; he is also a workaholic. He is not afraid to take risks to save a patient's life; this habit can occasionally get him into trouble. He has strong moral and ethical values, but he can also be self-righteous and a perfectionist at times. He apparently has a good relationship with his mother and siblings, although his long absences from Earth often lead them to complain that they rarely see him. His father - a famous general in EarthForce- has a domineering personality, and that has led Stephen to have a strained relationship with him. When they are together they frequently argue and they have conflicting views on a number of subjects. For example, Stephen's father is suspicious of aliens and believes that humans should "take care of their own", while Stephen believes that humanity should be more open to relations with alien races and civilizations. However, in many ways Stephen and his father are more alike than they will admit, and in the series second season they meet and begin to ease their differences. In terms of love and romance throughout the course of the series he has a number of love affairs with various women.
His most prominent and long-lasting affair is with "Number One," the attractive and tough-minded leader of the Mars Resistance. While the character was explicitly described as black in the script of the episode Soul Hunter, his first appearance on the show, J. Michael Straczynski was adamant throughout the run of the series that Franklin be a true individual who could have been played by an actor of any race. Richard Biggs later expressed his gratitude at being able to play a role purely as an actor, not a black actor.
Following in the footsteps of his father, General Richard Franklin, Franklin joined EarthForce in 2232 to become a physician. Shortly after graduating from medical school, he left EarthForce and spent the next three years "hitchhiking" aboard starships, trading his services as doctor for free passage to their destinations. In the course of his work, Franklin took detailed notes on the biology, physiology, and culture of many alien species. In his travels, he encountered a group of Minbari whose transport ship had crashed at Beta Durani. The Minbari were severely injured in the accident, and due to Franklin's lack of knowledge of Minbari biology, they all died. Franklin performed an autopsy on one of the Minbari, and gathered notes on their biology and genetics. When the Earth-Minbari War started in 2243, Franklin rejoined EarthForce and was assigned to manage an advanced military hospital on Earth. During the war, all EarthForce doctors were ordered to turn over any notes they had on Minbari biology for use in the production of biological weapons. When EarthForce discovered that Dr. Franklin had detailed notes on Minbari anatomy and physiology, he was ordered to give his notes to EarthForce researchers. Franklin, believing that it was unethical for a doctor to aid in research to create weapons of mass destruction, refused, and he was arrested by EarthForce. Franklin was released from prison shortly afterward to accompany Lieutenant Commander John Sheridan on a mission to the Epsilon solar system as part of an advance team to negotiate peace with the Minbari. They were ferried to the Epsilon system by a Narn warcruiser. The meeting with the Minbari was ended, however, by a sneak attack by the Centauri. They thought the meeting was for a weapons-shipment deal between the humans and the Narns. The Minbari delegate to the meeting was killed in the Centauri attack. Both Franklin and Sheridan (along with the Narn G'Kar), were captured by the Minbari. However, the Minbari surprisingly released them when Sheridan uttered a Minbari phrase that the Minbari delegate had told him before he died. After his release, Franklin returned to Earth; his activities for the remainder of the Earth-Minbari War are unknown. Between this event and 2258, he met Jeffrey Sinclair, the future Commander of the Babylon 5 station. It was largely on Sinclair's recommendation that Franklin was named the chief medical officer on Babylon 5.
In 2258, he was assigned to the Babylon 5 station as chief surgeon after the recall of Dr. Benjamin Kyle to Earth. He stayed there for four years. Franklin had strong moral convictions, and this was evident numerous times during his tenure at Babylon 5. Sometimes, his convictions conflicted with his duties as an EarthForce officer. These transgressions included the illegal operation of a free health clinic in Down Below, a part of the station where the poorest members of many alien races lived. He also insisted on performing a life-saving operation on an alien child against the parents' wishes; under the alien's religion any surgery was a violation of their religious beliefs. Franklin was devastated when the parents, acting according to their religion, killed their own child after the successful surgery. Dr. Franklin was also a leading participant in an "underground railroad" that helped rogue telepaths who had refused to join PsiCorps make their way to freedom; the telepaths were trying to escape from the ruthless Psi Cops. He was also a Foundationist, a new religion on Earth which incorporated the basic beliefs of many older human religions into a single faith. Foundationism (not to be confused with the school of philosophy called foundationalism), is a fictional religion invented by J. Michael Straczynski for his science fiction television show, Babylon 5. Foundationism appeared on Earth around the year 2157 in response to contact with other intelligent species in the universe. Dr. Franklin explains that "the idea behind the Foundation is that to get back to the roots of all the Earth religions, get past the doctrines to the core of each belief system to find out what they have in common. And they've got a lot more in common than you think. It's just when politics and money and nationalism get in the way that things get a little messed up." He also explains that Foundationists believe that "The closer you get to defining God, the further away it gets." As with many characters on Babylon 5, Franklin's personality contained the seeds of his own weaknesses. In his case, Franklin's passionate interest in saving lives and meeting a very high personal standard led to his use of stimulants ("stims") as shown starting in the third season episode, A Day in the Strife. Stims were a powerful but dangerous drug, and Franklin admitted his addiction obliquely to Delenn in Ceremonies of Light and Dark, and finally was forced by Garibaldi to confront this addiction in Interludes and Examinations. After he admitted his addiction, Franklin resigned as Babylon 5's medical chief and embarked on a walkabout of the space station (in the episode of the same name). The term "walkabout" comes from the aborigines in Australia; Franklin had learned of the practice from his Foundationist religious beliefs. In a later episode Franklin finally realized that he had run away from problems his entire life, and that he was doing so again. He finally confronted his problem, and although while on his "walkabout" he was nearly killed, he returned to medlab a stronger and wiser person for the experience. Although he spent most of the series in medlab saving lives, Franklin also saw his share of action and adventure during the series. He was an active participant in the Earth Alliance Civil War, where he aided the Mars Resistance in its fight to free the Mars colony from Earth control. During the war between the Centauri Republic and the Interstellar Alliance he also worked with the telepath Lyta Alexander in investigating reports of Drazi atrocities against the Centauri on the Drazi homeworld; both Franklin and Lyta were nearly killed during the investigation. In 2262, during the series fifth and final season, Franklin resigned from his post at Babylon 5 to accept the position of Head of Xenobiological Research on Earth upon the retirement of Dr. Benjamin Kyle. At the beginning of 2263, he selected Dr. Lillian Hobbes as his replacement on Babylon 5. Franklin later conducted research in the attempt to fight the plague the Drakh inflicted on Earth. He is seen in the Crusade episode "Each Night I Dream of Home."
At the end of the series, Franklin was still the head of Xenobiological research on Earth. When Sheridan learned he was dying, Franklin went to Minbar for one last party. From there, Franklin traveled to Babylon 5, where he witnessed the station's decommissioning and destruction. J. Michael Straczynski has said that Franklin eventually dies while exploring an unknown planet, but has not revealed the details of exactly how or when he dies. As Richard Biggs died in May 2004, the Franklin character will not make any further appearances in any future Babylon 5 movies or television series. When Biggs died, Straczynski had been working on a Babylon 5 script titled The Memory of Shadows. Straczynski decided not to recast the Franklin character, and rewrote the script to remove him from the story. In the Babylon 5: The Lost Tales anthology, it is explained that both Franklin and G'Kar - played by Andreas Katsulas who died in February 2006 - had left to explore space beyond the 'galactic rim'.