Captain Sheridan was appointed military commander of the Babylon 5 Space Station in Earth Year 2259, following Commander Jeffrey Sinclair who had become Earth’s first ambassador to Minbar. Given that the Minbari were co-sponsors of the Babylon Project, Sheridan was a controversial choice as many Minbari still referred to him as "Starkiller" due his actions in the war. This led to several incidents including a Minbari accusation of murder which threatened his command and career before Sheridan was fully accepted. Sheridan’s diplomatic skills and leadership led to the formation of an alliance of many galactic worlds which stood against an enemy known only as the Shadows. During this time Sheridan disappeared briefly on a distant planet known as Z’Ha’Dum and was rumored to have died when he detonated a nuclear device, destroying the Shadows’ chief city. His return from Z’Ha’Dum was seen as a miraculous return from the dead by some, and it is from this point that the legends surrounding him begin to appear.

The imposition of martial law on Earth by President William Morgan Clark, together with evidence of Clark’s complicity in the assassination of his predecessor Luis Santiago, saw Sheridan take the extreme action of declaring independence for Babylon 5. Strongly supported by the Minbari under their Ambassador Delenn, he formed a military force from other break-away Earth territories which was joined voluntarily by the alien worlds who had worked with him in defeating the Shadows. This force eventually caused the downfall of President Clark’s dictatorship. Sheridan’s breaking with military discipline during this time, his disobedience of direct orders from his Earth Force superiors, led President Susannah Luchenko, Clark’s successor, to insist on Sheridan’s resignation from Earth Force. Captain Sheridan did so only after guaranteeing amnesty for all who had fought under his command.

It was at this time that the newly formed Interstellar Alliance, drawn from the worlds that had followed Sheridan in the Shadow War and the advance on Earth, unanimously selected John J. Sheridan as its first President. A Minbari-Human military force known as the Rangers, which was under the direct leadership of Minbari Ambassador Delenn, also became part of the new ISA with its membership now open for the first time to all member races. The Babylon Station was designated temporary headquarters of the new Alliance until a more permanent headquarters could be built on Minbar. Following Earth’s joining of the ISA it was decided that an Earth Force commander should continue to govern Babylon 5 and, with Sheridan’s approval, this command was handed over to Captain Elizabeth Lochley*. It was at this time in late 2261 that Sheridan married Minbari Ambassador Delenn.

During the following year the Interstellar Alliance came close to cracking apart over the Centauri attacks on shipping and the retaliatory strikes of the Drazi and Narn fleets. Sheridan managed to hold the worlds together with the exception of the Centauri, whose new Emperor Londo Mollari withdrew them from the Alliance over the bombing of Centauri Prime.

With the new ISA headquarters ready at Tuzanor on Minbar, President Sheridan and Delenn left the Babylon Station towards the end of 2262. During the following year their only child David was born. Sheridan’s leadership of the Interstellar Alliance saw them through many early crises, including the Telepath War, and he was instrumental in saving Earth from complete devastation when the Drakh unleashed the plague which threatened Earth’s population. Sheridan’s leadership was valued so highly that the Alliance worlds repeatedly re-elected him to successive terms as President.

John J. Sheridan voluntarily stood down from the ISA Presidency in 2279 and the council of the Interstellar Alliance chose his wife Delenn to succeed him. Delenn had led the Rangers for many years and at her request Sheridan took over as their head, assuming her former duties as she took over his. He spent the next two years closely involved in leading and training the Rangers.