Meanwhile, a mysterious stranger named Morden came to the station asking, "Whaddya want?" The Centauri Londo answered his call: "To restore the Centauri to their rightful place!" Morden's reply: "Call us if you need assistance." Thus came the Shadows.
Some other stuff happened and eventually, season 1 ended. The Minbari ambassador Delenn revealed that Sinclair was captured at the Battle of the Line and interrogated. The Minbari discovered that Sinclair's body contained a Minbari soul, so it became necessary to stop the War. At the same time, Londo called on Morden to "assist" the Centauri in reclaiming an outpost from the Narn Regime. And back on earth, President Santiago was blown up....allowing Vice-President Clark to take over.
Later, Londo called on Morden to destroy the Narn fleet while the Centauri made the final strike on the Narn homeworld. And so the war was over. But the Shadow War had just begun.
Some more stuff happened and season 2 ended. The Centauri Republic continued attacking nearby races to form a "buffer zone," and Earth signed a non-aggression treaty with the Centauri. Vorlon ambassador Kosh revealed himself at last as...an angel.
Later, the B5 crew discovered that Earth had found a Shadow vessel buried on Io. Again, the Whitestar went to destroy the vessel. The new president, Clark, used this attack to declare martial law citing "alien influence in Earth culture." His secret security force, the Nightwatch, took over the Senate and ISN on Earth and Babylon 5 in space. Babylon 5 and several colonies seceded from the Earth Alliance and Civil War broke out. Eventually Clark won the battle and restored his control on Earth. Babylon 5 fell under Minbari protection.
Not long after, the Shadows started openly attacking the non-aligned worlds. In a show of force, the Vorlons counterattacked, and in revenge, the Shadows killed Ambassador Kosh.
It is revealed that Sinclair's soul was not just any Minbari soul, but in fact, that of Valen, a highly reveared god in Minbari history. This is explained by the fact that he goes back in time and becomes Valen. It also turns out that Delenn is a distant decendant of Sinclair/Valen.
Finally, Sheridan learned the reason behind the Shadows attacks.
Under Sheridan's command, the remaining first ones, the Minbari, the Narn, and the league of non-aligned worlds (basically everyone except the Centauri) confront the shadows and vorlons and basically boot them out of the galaxy. Lorien and all of the first ones follow them, leaving the rest to inherit the galaxy.
The now ex-patriot Babylon 5 staff (entirely human) decide take back earth and mars and depose the shadow influenced president Clark. There are plenty of left over Shadow and Vorlon technology used: the White Star fleet, Lyta, an army of Shadow modified telepaths, and Shadow tech modified earth cruisers. Sheridan and crew win.
Sheridan presents himself to the Earth government for disciplinary action and is forced to resign, but is named the president of The Interstellar Alliance which essentially puts him in the same position he was in when he was commanding the fleet in the Shadow war. Sheridan and Delenn get married.
We are given a sneak peak into the distant future where earth loses its way and discredits the efforts of Sheridan and The Interstellar Alliance and eventually nukes itself. But the rangers help recultivate the earth society. The humans appear destined to evolve into a Vorlon-like race; Sheridan's legacy lives on for millions of years, when the sun goes nova and engulfs the earth.
And so the story continues.