* The ending, particularly between Setsuna and Marina, bringing the Season 1 ending (Setsuna's letter to Marina) and Season 2 ending (Marina's letter to Setsuna) full circle.
** ''"We had, at last, finally come to understand each other."''
** One of the people shown in the epilogue is the girl who got half her body assimilated by the ELS earlier. She's alive and well, and looking damn good for a woman who's supposed to be in her sixties.
* Saji's devotion to Louise. She's [[IllGirl constantly ill]] and emotionally distant, but he never leaves her side.