The ending to the 2.55 story, specifically the banquet and it's disastrous aftermath
being framed for the 'assassination', seeing Minfilia and the Archons sacrifice themselves one after the other to allow the Warrior of Light to escape, it was just an emotional rollercoaster from beginning to end.
The part that really struck me emotionally though was probably after the Warrior of Light escapes from the tunnels at the Sil'dih Excavation Site, as that really drove home just how... horribly everything had gone wrong for them. That (narrative wise) they had no home, no livelihood, no allies, and were now on the run accused of a capital crime they didn't commit, I pictured Enki just about breaking down from the hopelessness of it all.
Of course things soon picked up when Alphinaud and Pipin showed up, but it still seemed that point was the Warrior of Light's darkest hour, as it was a direction in the story that I admit I had not expected SE to take. Grinding our seemingly invincible character down and showing their potential weakness in the worst way possible.
It was awesome stuff which will be a very hard act to top.