The opening narration for Season 2 Captain John Sheridan "The Babylon Project was our last, best hope for peace. A self contained world five miles long, located in neutral territory. A place of commerce and diplomacy for a quarter of a million humans and aliens. A shining beacon in space - all alone in the night. It was the dawn of the Third Age of Mankind - the year the Great War came upon us all. This is the story of the last of the Babylon stations. The year is 2259. The name of the place is Babylon 5."

With the death of Earth Alliance President Luis Santiago, Vice-President Morgan Clark now takes over as the new President. And immediately things begin to change. As the season opens Sinclair has been recalled to Earth, and then sent onto Minbar as the new Earth Ambassador. The suggestion is that Sinclair might know too much about Santiago's death. Michael Garibaldi is still in a coma, and Lt. Commander Susan Ivanova is temporallily running the station. And of course Ambassador Delenn is still in her Cocoon! President Clark appoints Captain John Sheridan - a war hero - as the new commander of Babylon 5. It was Clark's hope that Sheridan would follow a more pro-Earth anti- alien policy. President Clark is connected with the Psi-Corps, the organisation responsible for the training and control of human telepaths. It is starting to become clear that the new President is taking the government in a sinister direction. A renegade Minbari Battle Cruiser is on the loose and it is Sheridan's first job to deal with it. Delenn comes out of her cocoon as a very beautiful Human/Minbari hybrid. Garibaldi revives from his coma and with the help of Psi Corps rep Talia Winters is able to recall who his attacker was. And the plot thickens as President Clark becomes involved. G'Kar brings news of a terrible new enemy. Because Sheridan was a war hero, Earth Government imagined he would be more favourable to their increasingly dictatorial policies. But as time went on, Sheridan and his colleagues- including Commander Susan Ivanova, Security Chief Michael Garibaldi and Doctor Stephen Franklin - began to learn sinister truths about Earth's new world order, most importantly that the new president, Morgan Clark, was responsible for the assassination of his predecessor Luis Santiago. With the newly formed Ministry of Peace and the Nightwatch organisation, Clark's government was becoming ever more powerful and intrusive in the lives of the people on Earth. Meanwhile, Sheridan began an unlikely but close relationship with Delenn, which was to grow into an enduring love story. When Sheridan was alerted to a conspiracy to destroy Earth from within by his old friend General Hague, he decided to form a small conspiracy of light to learn about and oppose Clark's take-over bid. Centauri Ambassador Londo Mollari's alliance with the sinister Shadows helped his political associates assume power within the Republic. They also forced the Narn Regime to declare war on the Centauri. "For a hundred years the Centauri occupied our world, devastating it. We swore we would never let that happen again. This attack on our largest civilian colony has inflicted terrible damage and loss of life. They've crossed the line we can not allow them to cross. As a result two hours ago my government officially declared war against the Centauri Republic. Our hope for peace is over. We are now at war. ... We are now at war." G'Kar: "The Coming of Shadows". The Narn were almost totally destroyed following a brutal attack on their home world. Using huge black spider like ships, the Centauris' new allies gave occasional help in attacks on the Narn, while the Centauri used devastating weapons called mass drivers on the Narn Homeworld in what Londo understood would be the first steps towards the resurgence of the once great Centauri empire. Despite the appalling and illegal nature of the destruction of Narn, Earth Alliance had even negotiated a non-aggression pact with the Centauri, which Sheridan realised undermined Babylon 5's neutrality. As human sightings of the black ships increased and G'Kar discovered prophecies relating to them, Delenn revealed the truth to Sheridan. "There are beings in the universe billions of years older than either of our races. Once, long ago, they walked among the stars like giants, vast, timeless. Taught the younger races, explored beyond the rim, created great empires, but to all things, there is an end. Slowly, over a million years, the First Ones went away. Some past beyond the stars never to return. Some simply disappeared ... Not all of the First Ones have gone away. A few stayed behind, hidden, or asleep, waiting for the day when they may be needed. When the Shadows come again." Delenn: "In the Shadow of Z'ha'dum". The aliens, known only as "Shadows" were one of the first races to exist in the Universe, the "First Ones" who also included the Vorlons. The Shadows were also extremely hostile, having fought a long war against many younger races, including the Minbari, a thousand years ago. Sheridan agreed that Babylon 5 would join the Army of Light against the Shadows. Realising that the Narn-Centauri war was merely a harbinger for events to come, Sheridan welcomed the support of Draal - the custodian of Epsilon 3 and its advanced technology. Sheridan was also given joint control of all Rangers in the area by Delenn. Ambassador Kosh summoned an inquisitor to determine whether Delenn is right to ally herself with him during the coming war against the Shadows. The inquisitor, Sebastian, tortures, taunts and degrades Delenn until Sheridan comes to her rescue. When Sheridan and Delenn demonstrate that they are willing to sacrifice their lives for the other and die unnoticed and alone, Sebastian tells them that they are the chosen ones: the right people in the right place at the right time. They are also the first to pass his test. At the close of 2259 the Centauri aggression had brought Babylon 5's peacekeeping mission to an end. However, the nature of the Vorlons seemed to become clearer as Kosh left his encounter suit and appeared as a being of light flying up to catch Sheridan as he fell from a sabotaged core shuttle carriage whilst en route to a meeting of the Advisory Council in the Zen Garden.

Final Note of Season Two Spoken by Commander Susan Ivanova "We came to this place because Babylon 5 was our last, best hope for peace. By the end of 2259 we knew that it had failed. But in so doing, it had become something greater. As the war expanded, it became our last, best hope for victory. Because sometimes, peace is another word for surrender. And because secrets have a way of getting out".