For me personally, it's the entirety of the Trooper story and chapter 2 and 3 of the Imperial Agent story.

The biggest reason as to why i find Trooper to be the most memorable story is that i just like militaristic things in general. Another reason for me are both chapter 1 with hunting down Tavus and the rest of the traitors AND chaoter 3 with taking down Rakton for good. While yes, the story has issues but in the end of the day it made the most fun and is the most memorable for me.

Now, to Imp Agent. Honestly, Chapter 1 is not as memorable for me since, but chapters 2 and 3 are for me. I olve "working for the Republic" as Legate in chapter 2 (and often when i create a Imp Agent, i roleplay them as double Agents that work for SIS). And chapter 3 with taking down the Star Cabal is very interesting, the idea that don't want both Jedi and Sith "ruling the galaxy" and how they became corrupted, hence why i find it very memorable.