How did *spoilers*

This was all explained in the Centauri trilogy of books.

Just in case it was not obvious I have added spoiler tags.

The scenes from the movie "In the Beginning" are not the same as the scenes from episode S05E19 "The fall of Centauri Prime".

In episode S05E19 you see how the alliance attacks Centauri Prime, how Londo becomes emperor and how the Drakh becomes the main player. In the movie you can see how the Drakh are taken out by the Centauri resistance (led by Vir).

This is all explained over the course of three books, so I will skip some details but here's the summary:

When the Drakh found out that Delenn was pregnant of Sheridan's son they started a long term plan (they are nothing if not patient). They wanted to plant a keeper on David same as Londo had. They placed a keeper in the urn that Londo gave to Sheridan in S05E21. Londo was unable to warn Delenn and Sheridan because of the keeper. Londo could only control his keeper through large amount of alcohol, which of course where not available.

Years later Sheridan gives the urn to his son, and the keeper manages to attach himself to David. The keeper then manages to convince David to go to Centauri Prime.

Once there David falls in the hands of Londo and the Drakh. With David in their hands the Drakh are now planning the final stages of a massive Centauri/Drakh atack against the insterllar alliance.

Meanwhile Londo invites Delenn and Sheridan over to get back David. The keeper thinks that Londo will kill Delenn and Sheridan therefor he allows it. However, Londo manages to get properly drunk and helps Delenn and Sheridan to escape in exchange for assistance in getting the Drakh out of Centauri Prime.

Meanwhile Vir has been leading the resistance. When he hears about David he speeds up the plan to attack the main base of the Drakh. He attacks the Drakh tower destroying it. This also makes public the presence of the Drakh to the Centauri public, the military and the Insterstellar Alliance. Crucially the Centauri military instantly stop their planned attack against the alliance and attack the remaining Drakh with alliance assistance.

Unfortunately the Drakh had an ace up their sleeve. They had planted bombs all across Centauri Prime, similar to what Londo did to the Shadow infested island of Selini. When it became obvious they had lost Centauri Prime they blew up the bombs, that's why Centauri Prime is burning in the movie.

The Centauri Prime trilogy is very much worth reading. However, in particular part 3 can be hard and expensive to find. However, there is also a hardcover omnibus that combines all books in one. That is also hard to find, but often cheaper then just book 3 individually!