CP9's Independent Report is the tenth Cover Story created as a side story on the title pages of each One Piece chapter. The story is set after the events of the Enies Lobby Arc and before the Dressrosa Arc.
With the money they gain from this, they admit Lucci to a hospital, where he remains unconscious for a few days, while the other agents spend their time shopping and sightseeing. After his recovery, CP9 goes to a bowling alley. There, a commotion outside alerts them of the invading Candy Pirates, whose captain captures a mother and daughter. CP9 then arrive and defeat the Candy Pirates with ease, as the townspeople look on in amazement. However, Lucci deals "excessive justice" to the crew's captain by crushing his head with his foot, causing the citizens to run away in fear. Knowing that they can't remain on the island anymore, they prepare to leave the island, but before they do, a girl comes up to them and presents Kalifa with a beautiful flower as thanks for saving her and her mother.
CP9 returns to their homeland, where they witness a future generation of Cipher Pol is being trained. The Marines, being lead by Captain Very Good, show up to capture CP9, but they fiercely protect their home, quickly dispatching them. Spandam, in his intensive care unit, receives a Den-Den Mushi call from Lucci, who says that someday they will return for him - likely for revenge, since Spandam was the one who blamed CP9 for the failure of the mission and sent the Marines after them. They are on a hijacked boat with the body parts of Very Good left scattered behind. Panicked, Spandam and his father, Spandine, then plot the obliteration of CP9.
The agents of CP9 then leave their home island, sailing off into the distance with the flower of beauty and goodwill symbolically planted in the earth of their childhood home.