Presumably following on from the events of the Legacy of Kain: Defiance Comic (but not the conclusion of Soul Reaver 2), Chapter 1, showed Kain's initial attempts to infiltrate the stronghold. Kain re-materialized from his Bat Form on the roof and proceeded to find his way through the Sarafan Stronghold.
Some aspects of this sequence relate to other chapters in the series:
"Archive footage" from the opening cinematics of both Legacy of Kain: Soul Reaver and Soul Reaver 2 is used in the prologue sequence.
Chronologically, this chapter depicts Moebius's earliest known interaction with Kain. When Moebius muses that "it has been a long time" since he and Kain met, he is probably speaking in terms of Kain's personal timeline, not his own. From Kain's perspective, his and Moebius's most "recent" known meeting occurred in The Vampire Purges (chapter) of Blood Omen: Legacy of Kain (the Blood Omen era).
Moebius seems to make an oblique, and sarcastic, reference to the events of Blood Omen: Legacy of Kain when he mentions that Kain "there was a time when [Kain] might have heeded wise counsel when it was offered". In Blood Omen: Legacy of Kain's Find the Oracle, Kain elicited Moebius's counsel to continue his journey. He followed all of the advice given to him, but the end result was the near-extinction of the vampire race.
Kain has the main objective "Hunt Moebius down within the Stronghold" and the minor objectives "Enhance Reaver to destroy barriers", "Destroy the blessed barriers", "Seek out Moebius' chamber" and "Destroy Shades and pursue Moebius". Prima's Defiance Guideparaphrases the main objective as the Chapter title "Infiltrate the Stronghold" but beyond this it only mentions the first minor objective, paraphrased as "Acquire the hub of the Balance Emblem".
Dialogue implies that the beginning of Defiance follows on from the events of Defiance comic. Developer comments and structural changes in the Stronghold show that it is set some years after the conclusion of Soul Reaver 2.
Prima's Defiance Guide goes into great detail naming rooms and sections of the level, providing a detailed layout of the Sarafan Stronghold, these rooms are: "Street", "Dungeon", "Wall Cavity", "Main Battlements", "Cloister" (SR2'sCourtyard), "Sanctuary Entrance", "Sanctuary" (SR2'sSarafan Cathedral including the Chapels dedicated to William and Janos), "Chapter House Entrance", "Chapter House" (SR2'sSarafan Memorial Chapel), "Small Battlements", "Training Area", "Small Drawbridge", "Staircase", "Cistern" and "Moebius' Chamber".
This chapter extensively features Sarafan designs throughout the level, some in the very masonry itself. The mysterious Lovecraft's Diary script is also featured heavily throughout the stronghold, perhaps more so than in any other location in the game. At the end of the chapter, Moebius is shown conversing with the unseen Elder God using a large rock carved with an hourglass.