The five most popular story-related questions people ask about Devil May Cry Season 1, Episode 3 'The Deep and Savage Way' are:

1. Is Vergil alive, and how does Plasma's ability to copy living beings relate to him?
2. What is the significance of the White Rabbit character, especially regarding his resilience and possession of part of Vergil's amulet?
3. Who are the new villainous characters introduced (Echidna, Cavaliere, Plasma, Agni, and Rudra), and what are their roles?
4. How does the explosive implanted in Dante affect the plot and his capture?
5. What are the implications of the different animation styles used for the demons, and how does that affect the storytelling?

These questions arise from key plot points and character developments revealed in episode 3, such as the revelation about Plasma needing a living version to copy, the mysterious status of Vergil, the introduction of the villainous cast, and the dynamics of Dante's struggle and capture.