Apollo is both Newo Ikkin's and The Writer's dog, both in the real world and in Heaven's Fence.
The Second Stage Turbine Blade Edit
Apollo remains in the background for Second Stage Turbine Blade, making only minor appearances. He's mentioned briefly by Claudio in the Junesong Provision, the letter he left behind for Newo.
In Keeping Secrets of Silent Earth: 3 Edit
Ten years after Claudio's disappearance, he returns to Newo's home, trying to find the courage to speak to her and explain the whole of events that have occurred since he left. He fails to do so and is confronted by Apollo, who mistakes him for an intruder at first before happily recognizing the bearded Claudio. He spends the night outside with Claudio, who explains the circumstances that lead to him leaving Newo and begins to tell the whole story he had planned for Newo to Apollo instead, as he has the courage to talk to the dog. Going through every detail that came to mind, Claudio eventually came to the conclusion that he needed to move on and face destiny, which did not involve Newo. Telling Apollo goodbye, he started to leave, only for the dog to follow him. He told the dog to stay, stating that where he was going the dog could not followed.
Good Apollo I'm Burning Star IV, Vol. 1 - From Fear Through the Eyes of Madness Edit
In The Real, Apollo is the loyal dog of the Writer, who is descending quickly into madness. This is ultimately staved off with assistance from Ten Speed of God's Blood and Burial, who drives him to murder Ambellina in the Fiction, mending his damaged mind.
In The Fiction, Apollo remains with Newo Ikkin, having not followed Claudio when he departed at the end of In Keeping Secrets of Silent Earth: 3.