In the last couple of chapters, just seeing Aki back in control of his body and being on the side of Aya and her friends is enough to be heartwarming, given how he'd been nothing but a shell for the Progenitor for goodness knows how long. It's only temporary, but still.
Ceres taking over Aya's body, and then taking Shouta - a sick boy unable to walk - flying. Most of the times we've seen Ceres so far, she's either been on a murderous rampage or acting very coldly, so seeing her taking Shouta flying for no ulterior motive is very sweet.
When Tooya crashes a helicopter into the Mikage headquarters to get to Aya, Alec shields Aya's unconscious body with his own. And this is after Alec refused to alter Aya's memories.
Tooya and Aya, finally back together again. The chip that caused Tooya a raging headache if he tried to remember Aya is broken, both are safe in Alec's secret lab and they can finally be together. For real, including Tooya asking Aya to come with him, so they can search for his real memories and her hagoromo. It's also a tearjerky scene, but mostly just makes one feel fuzzy.
Towards the ending, the goodbyes the members of the C-Genoma project give each other as the project is being shut down and Kagami is leaving with Ceres. Especially the one between Alec and Lulik, considering Alec should have been seen as a traitor for attempting to back out of the project.
Assam: Chief! Me too, I want to be with-
Kagami: No! Assam, go with Lulik. Go to school and to college. Your face is too cute to belong to an assassin.
Lulik: [To Alec] Alec, I'll be praying for you! We'll meet again.