After Unit Zero was destroyed in battle with the Angels, the soul of Naoko Akagi was finally freed. But the elder Akagi was too stubborn to go quietly. She had unfinished business to attend to. She had to get revenge.
- Adaptation-Induced Plot Hole: A relatively minor one, due to the author taking some incorrect Fanon about Unit 00's soul as Canon for this story.
- Back from the Dead: Well, sort of. Considering this is a story about Naoko Akagi as the Spectre, this should come as no surprise to anyone.
- Be Careful What You Wish For: Keel, who seeks immortality will now (to borrow a phrase from Gargoyles) live as long as the mountain stones.
- Buy Them Off: Keel tries this. It doesn't work.
- Darker and Edgier: Than the other stories in the series.
- Giant Space Flea from Nowhere: Eclipso.
- Karmic Death: The fate of Seele 05.
- Mama Bear: Downplayed with Naoko.
- Pay Evil unto Evil: The whole point behind The Spectre, and it holds true here as well.
- Reality Warper: The nature of The Spectre's powers.
- Revenge Before Reason: Naoko warns Gendo and leaves him for last to make him sweat. It backfires on her.
- Roaring Rampage of Revenge: This story is about Naoko becoming the the spirit of vengeance, after all.
- Sins of Our Fathers: Naoko tries to enact revenge on Rei III over what Rei I did. It doesn't work.
- Woman Scorned: Naoko is all over this trope.