Upon their arrival in a different time period, Zephyr One started to fall, before its autopilot pulled them out of the dive. Once they landed, Rodriguez asked where they were, and they discovered that they had jumped to 1955 and were just outside of Area 51. They discussed how the time travel worked, and figured out that the Chronicoms were after Project Helius, as that could stop S.H.I.E.L.D. from going after them.

Still, a Spider-Man isn’t a real Spider-Man without at least some tragedy. This time around, Prabhakar refused to help a woman being mugged. This led his Uncle Bhim to intervene and—like so many of Spider-Man’s parental figures before him—he died as a result. In the end, Prabhakar learned that with his great power comes great responsibility. The team later gathered to celebrate the retirement of Phil Coulson. They reminisced over their different homes, with Rodriguez wishing she had met the team earlier. Yeah, but that was before I started hunting someone with Coulson's face." ― Melinda May and Yo-Yo Rodriguez [src] You won't listen. I'm in a nightmare, and I'm screaming at the top of my lungs, and none of you can hear me!"While the others went out to investigate the Chronicom's recent actions, Rodriguez and Simmons watched as Enoch treated May in the Healing Pod. Rodriguez questioned if they could trust Enoch as he was not a human, but Simmons assured her they could as he was the reason she was alive. Simmons stated that May would make a full recovery, and then informed Rodriguez that her body was breaking down the Shrike material, and would soon be completely out of her system, much to her relief. Yeah, good thing we brought the really small plane to carry all of them." ― Lincoln Campbell and Yo-Yo Rodriguez [src] May decided to spar with Rodriguez, which she preferred. May tasked Rodriguez with trying to beat her by avoiding her hits with her powers. Instead, Rodriguez became thrown with various emotions and memories overwhelming her, including getting infected by the Shrike, Tess' death, and when she murdered Ruby Hale. Rodriguez opened up about killing Hale, saying she acted on impulse. May then continued to fight Rodriguez, which had her remember a memory from her childhood, which caused her to cry. My heart was beating so fast, I thought someone had put cocaine in my beer." ―Yo-Yo Rodriguez and Flint [src] Stonewall insisted on staying at her side while she struggled with the devastating injuries, but Rodriguez later gained two prosthetic limbs to replace the originals. At that time, she and Stonewall also helped each other face their respective parents, and the team banded together to convince Daisy Johnson to reinstate Druid after she’d dismissed him from duty.

Later, Prabhakar returned for SPIDER-GEDDON (2018), playing a relatively minor role as part of Miles Morales’ Spider-Army. In the end, Prabhakar helped transfer the minds of the Inheritors to the bodies of newborn babies, giving them a chance to be better than they had been in their previous lives. He also returned for the “End of Spider-Verse” arc in SPIDER-MAN (2022), where he helped defeat Shathra, an evil wasp goddess dedicated to killing those with spider-based powers. Rodriguez kept hidden in Zephyr One as Jaco searched for her. She used her powers to steal his gun and handcuff him. However, he broke free and told her he didn't want to fight, saying he was trying to save their planet. Rodriguez asked if he fine with all the killing, but he stated he just wanted to kill Izel, so the two decided to work together. Rodriguez and Deke Shaw were tasked with retrieving a device from Niles Lindmore and deliver it to Phil Coulson, who was on a mission with Daniel Sousa. Rodriguez noticed that Shaw was quiet during the drive, and they talked about how incredibly sexist and racist the past was, which Rodriguez told Shaw got better, only slowly. Shaw noted that they couldn't make any big changes, due to messing up the timeline, which made Rodriguez feel like they were just "Agents of Status Quo." May took Rodriguez to the Quinjet and scolded her for stealing the director's badge, mentioning how she makes a terrible spy. Rodriguez tried to deny taking the badge, but May revealed that she knows everything that she had been up to, including the facial recognition search. Rodriguez gave up and handed May the badge, with the latter telling her to be less sloppy next time. Keep collections to yourself or inspire other shoppers! Keep in mind that anyone can view public collections - they may also appear in recommendations and other places.May, these guys started shaking and screaming as soon as we put them together." ―Yo-Yo Rodriguez to Melinda May [src]

It's spreading. Passports, visas. Somebody's taking the Watchdogs global." ―Yo-Yo Rodriguez and Phil Coulson [src] Sounds like I missed a lot. I was only in here for a few minutes." ― Phil Coulson and Yo-Yo Rodriguez [src]When Rodriguez came across Melinda May, she was told that whether she made the right decision was up to her to decide, and that she had to make peace with it and with how people would from see her. Upon learning that Johnson was finding a way to save Coulson, Rodriguez revealed how she hd spoke with herself in the future, who said saving Coulson was what caused them to fail. May disagreed with this, but Rodriguez was sure of what she was told, but was interrupted when Coulson realised the aliens had the ability to teleport inside.