In Issue 37, Zero, investigating an explosion, teleported in and grabbed one of the two people responsible. He then dissuaded X of coming close to becoming Maverick when the latter warned him that the two perps, although dangerous, were still human, and preempted X's thanks for saving him. Zero also explained the history and motives of the group the two people belonged to, the Emerald Spears. He later appeared in the next issue, as part of a task force (which also included Vile and three unnamed Reploids), saving X from the Wily Walker. He then told X to go to Dr. Cain to see if he discovered any weaknesses in the Wily Walker while they try to stop it. Issues 39 and 40 saw Zero and his allies-including X and Sigma-continue their efforts to halt the Walker, though Vile angered Zero by launching an attack that endangered nearby civilians. Eventually the Reploids succeeded in defeating the Walker for good, though Zero was instructed by Sigma to keep his eye on Vile.
Fighting Sigma and Worlds Unite
Eventually, after Sigma turned Maverick, Zero remained to lead the Maverick Hunters. On the Day of Sigma, Zero was demanding for various hunters to down the list until they find someone, and that they should also get Flame Mammoth on the line just as X was arriving at the Hunter HQ. He then learned that not only was there no response from either Flame Mammoth or anyone within the 4th Overland Unit, but there were reports coming in that the 6th Marine Unit had joined Sigma's forces, much to Zero's shock. He then noticed X and demanded to know Dr. Cain's status, with X confirming as far as he knew that he's all right before asking Zero what was going on. He then informed X that Sigma went maverick. In large part due to the stressful events of that day piling up, Zero then launched into a rant towards X when the latter implied they should contact Sigma to find out the truth and end the affair peacefully that Sigma had bombed Arcadia, left it in flames, had recruited several units of the Maverick Hunters to his side and had them attack those still protecting humanity, and that Sigma had just threatened to launch nuclear weapons before bluntly telling X that there is no peace to be had before ordering for him to take shelter. However, X instead joined Zero's efforts, citing he has one more hunter on his side now. At some point he was somehow involved in saving X from the X-Hunters under what was presumably a very challenging fight against X. Eventually, under "complicated" circumstances, Zero and X ended up fighting each other.
Zero would later take part in the Worlds Unite crossover event, joining his fellow Maverick Hunters in teaming up with Mega Man, Sonic the Hedgehog and other heroes in battling an alliance led by Sigma. He and his fellow Hunters first appeared in Sonic Universe Issue 76, where they attacked one of Sigma's fortress in a final bid to take him down once and for all. He, alongside Axl, initially was going to accompany X to confront Sigma, although because of an ambush set up by the now-Maverick (and repeatedly-revived) Vile, Zero and Axl elected to stay behind to hold Vile off (with Zero in particular expressing irritation at how "mouthy" Vile gets after each revival). Ultimately, the Hunters secured the base, although their primary objective, stopping Sigma, was a failure due to Sigma escaping at the last minute via a portal, also cryptically hinting that he'll soon conquer several worlds just before escaping. After securing the base, Zero, alongside X and Axl, met Silver the Hedgehog, a resident of a different dimension, who was trying to close the Genesis Portals.
After Silver subdued Vile, he then gave them the coordinates of where Sigma might have gone after analyzing the computer and opened a portal for them. However, the portal instead took them to an alternate reality to that dimension. As the portal closed off behind them just as Zero suggested going back upon learning they went to the wrong dimension, X elected to try and find locals to inquire where to find another portal-creating device. However, one of the locals, Sticks the Badger, witnessing them and believing them to be invaders, proceeded to attack them (also hitting Zero in the head with a boomerang), although X managed to explain to her that they were actually cops trying to capture a criminal who escaped to a different dimension. Sticks then, after learning their true reason for coming, decided to aid them and took them over to Dr. Eggman's lair to use dimension-transport technology there (also strongarming Comedy Chimp and Fastidious Beaver to help, to Zero's annoyance). When encountering two robot locals who attempted to ward them off, Zero in turn proceeded to threaten them into opening the portal, to X's concern, although they nonetheless managed to get to the portal.
The unlikely team eventually made their way to Mega City as it was in the process of being fused with Mobotropolis, home to Sonic the Hedgehog. The team then joined up with the Freedom Fighters and Robot Masters of the two merging worlds, and after determining that Sigma was behind the incident they boarded the Sky Patrol. A meeting was soon held aboard the craft, and Zero joined Break Man in collecting X, Mega Man, and Roll. Their group was later unexpectedly joined by Dr. Wily, Doctor Eggman, and Xander Payne, who informed them that Sigma had established himself on the Lost Hex. On the way there, Wily noted that Zero seemed like something he would build-unwittingly recognizing his future role in Zero's creation-while Zero befriended fellow swordsman Antoine D'Coolette. Unfortunately, the heroes soon found themselves contending with a new adversary: the Deadly Six and an army of Mechaniloids.
During the fight, X and Zero recognized several of Sigma's former mindless minions, and realized that he must have revived them using the power of the Genesis Portals and Unity Engines. They set about destroying them, focusing on them at the expense of the Deadly Six, who forced them, the Robot Masters, and Gemerl to attack their friends. Axl briefly panicked, fearing that they were going Maverick, and Zero helped him realize that their situation was different and encouraged him to do what he could to resist harming their friends. Fortunately, they were soon freed by the Egg-Wily Uppity Robot Scrambler Cannon, which also subdued the Deadly Six. Determined to stop Sigma before he gained any more ground, Zero urged that they press their assault, something that Sonic agreed with. However, their allies were of a more cautious mind, recognizing that battling the Mechaniloids and each other had left their group severely weakened. Unfortunately, Sigma soon unleashed his latest army: a force made up of Maverick clones that emerged to accompany their master in his massive new body.
During the ensuing struggle, X made a point of checking on Zero, given that Axl had been somewhat concerned at facing what appeared to be resurrected enemies and friends. Zero recognized the doppelgangers for what they were, however, and further noted that Colonel and Iris weren't part of the attacking force. Sadly, the heroes proved too weak to take on the villainous horde, and the majority of them scattered at Sigma's bidding to invade other worlds. Burn Rooster, Double, Dynamo, and Vanishing Gungaroo remained behind to finish them, but were unexpectedly taken down by a new group of allies: heroes from the world of Street Fighter. Inspired by Sticks' idea of recruiting these new allies, Sally Acorn directed the growing army of heroes to split into teams and follow the Mavericks. Their objectives: stop the villainous robots from planting more Unity Engines, and recruit more allies to join in the battle against Sigma. Zero and Bunnie Rabbot then departed through a Genesis Portal, specifically the one leading to the world of Ghosts 'n Goblins. After Bunnie explained to the irate and confused archdemon Astaroth that the Mavericks Zain and Geemel were planning to steal his world's energy for Sigma, it resulted in the Mavericks being incinerated by the demon, and forcing the dark lord to call a truce with the knight Arthur (whom he had entered a duel with earlier via his right hand demon Firebrand) to deal with Sigma in response, also sending Firebrand to aid Arthur and the others. He then returned to the unified world with the others and reunited with everyone to proceed to fight with Sigma and his Mavericks.
Prior to his formal debut, Zero appeared in issue 34 in its Short Circuits, where like X, he was excited about appearing in a Mega Man comic until Mega Man and Roll escort them off the premises. He would later appear in issue 38's crossover, spotting a despondent Roll watching Mega Man and X going off together. Giving Roll a helmet identical to his own, he invited her to join him on an adventure of their own.