Episode 3: On Your Marks starts right where episode two ends, Alto, Ranka and Sheryl stand together as Ozuma and the skull squadron launches to intercept the newest Vajra attack. After another dome breach Alto, Ranka and Sheryl find themselves locked in an emergency escape pod, the three get to spend some quality time together. This episode really brings back memories of SDFM episode 4 Lynn Minmay but instead of a giant tuna head we get Nyan Nyan tuna buns.
During the battle Ozuma gets injured after assuming Mikhail's headshot killed the Vajra, the NUNS send a squadron of VF171 valkeries in to assist. Meanwhile life support cuts out in the trio's escape pod and Sheryl decides to take matters into her own hands, but just as she's about to open the latch to a possible space vacuum the three get rescued by Grace and Cathy Glass, the Skull Squadron returns to the Frontier and reports that Ozma has been injured, both Cathy and Ranka are very troubled by this news and when they see Mikhail and Luca assisting Ozma's valkerie back to the hangar Ranka breaks down and cries hysterically. Inside the hospital we discover a bit more of Ranka's past, how her entire family along with a thousand others were killed by a Vajra attack on the 117th Large Scale Research Fleet. The SMS medical officer Kanaria Bernstien explains that Ranka has dissociative amnesia. Ozma tells Alto that he isn't really Ranka's brother but he keeps the truth from her to protect her. Alto becomes enraged and demands answers, Ozma gives him twenty four hours to think it over.
The next day Alto is walking thru a park and hears Ranka singing, She tells him it's the only memory she has of her childhood, and after yesterdays events wished everyone could hear it. Alto tells her she can't if she simply wishes for it. So with Alto's motivation Ranka sings her song, which in turn motivates him to join for SMS.
Episode 3 ends with the burial ceremony of NUNS pilots in a miltary graveyard contrasted by the SMS ceremony for Gilliam. Alto waits outside and when Ozma and the Skull Squadron are leaving the ceremony Alto gives Ozma his decision and Ranka is seen in front of an interview panel as she persues her dream of becoming a singer by entering the 12th Miss Macross contest.