On the back of the title Secret Wars., it gained its own weekly title, Spider-Man and Zoids. The comics anthology included reprints of Spider-Man stories and an original series of Zoids tales. The latter has no continuity with any Japanese anime (which didn't exist at the time) and it was created to go along with the original UK (and subsequently Australian) release of model kits.
On the outer rim of the Zoidaryan Empire, battlefleets still patrolled their subdued populations, periodically returning to the home system. One such battlefleet miscalculated its return, and crashed onto the Blue Moon of Zoidstar. There was a single Zoidaryan survivor, pulled from the wreckage by android technicians, and given a protective exoskeleton to restore his crippled body.
On the icy moon, the marooned Zoids were incapacitated by the frigid temperatures, and the androids set about converting them to more resilient forms. It was the conversion of heating up the Zoids for survival that turned them from their original blue to red: the Red Zoid mutants were born. Eventually, the surviving Zoidaryan returns to Zoidstar to find that his people have apparently been wiped out, and that automated factories have produced legions of Zoids that continue to battle on, even though their creators have disappeared.
Realizing that he is the last of his kind, the Zoidaryan adopts the moniker "Namer", and gives each of the warring machines an apt title to describe its capabilities, for example: "Small and fleet of foot, yet cunning and deadly in battle; thus I name you Spiderzoid." With his naming, the Namer issues a stark prophecy, that when the remodelled Zoids from the Blue Moon return, there will be an ultimate battle.
The Red Zoids, led by Redhorn, land on Zoidstar and attempt to seize control of it. Threatened by these outsiders, the Blue Zoids temporarily cease their combat and unite under the mighty Zoidzilla to drive them off. Total war breaks out, with Redhorn forcibly converting Blue Zoids into red. He soon gains a general in Mammoth, a Blue Zoid traitor who willingly converts to Red.
Into this melee crashes the Celeste, a terran starship, in the year 2274. The crew were transporting prison convicts to Zoidstar, believing it to be an uninhabited world where they can build a prison. The ship is blasted out of the sky by a fireball, stranding a few survivors on Zoidstar. Under the command of Captain Drew Heller, they are band together and are joined by the Namer, and they attempt to survive and escape Zoidstar. Early on, they manage to capture a Spiderzoid and Heller's son Griff becomes its pilot - being the only one who can fit in it - to defend them against other Zoids.
While the Blue and Red Zoids clash, a third force is looming over them. Krark, the ultimate Red Zoid mutation and proclaimed the Prince of Darkness by the Namer, is attempting to band together all the Zoids. While the two armies are content to beat each other to oblivion, Krark wants to leave Zoidstar behind and build a new Zoid Empire, ruling over the entire Galaxy. He has some success but his plans face resistance from the fact that most of the Zoids don't understand his ideals and just want to continue fighting each other.
Plots would be split between the machinations of Krark, the battles between Blue and Red Zoids, and the humans attempt to survive. There were occasional offbeat tales. One story of an elderly Cosmozoid who, tired of fighting, searches for the fabled Metalon where Zoids go to be granted eternal peace; too late, he discovers that Metalon is actually a place for Zoids to spend an eternity of unending combat, and he is trapped forever. Another story had an android realising the horror of what the Zoid's had done to the planets they conquered for the Zoidaryans, but was reduced to impotent protests as his comrades continued their war around him.
The strip later reveals that Silverman, the head of the convict program on board the Celeste, is actually an android, in much the same vein as The Terminator and Ash from Alien. He attempts to kill the crew when discovered and be the only one to escape Zoidstar. It turns out that the Earth government and the corrupt Cybersol Corporation knew about the Zoids and the Celeste mission was intended to use the crew as guinea pigs, prior to a full-scale operation to capture & duplicate the Zoids for military purposes. Heller and Silverman battle in an abandoned Zoid production facility and it is believed Silverman is dead.
Other stories would reveal a second surviving Zoidaryan - Clada - who is self-proclaimed commander of the Blue Zoid army (though considered a mere factory commander by Zoidzilla). An annual story would show Namer and Clada knew each other of old, with the former building the invincible Zrk Zoid that Clada piloted to victory over victory. Clada's arrogance led the Namer to challenge him to Heroic Combat and - knowing Zrk's weak points - defeat him. Their feud would come to head in the present day, with Namer winning but losing the trust of the Celeste in the process.
Meanwhile, Mammoth tricks Redhorn into being gunned down by both Zoidzilla and Krark, assuming command of the Red Zoids in the process. Redhorn's android survives though and attempts to rebuild his Zoid form, battling the Celeste crew in the process. As the humans gain control of the Zoid Great Gorgon, Heller is plagued by nightmares of Silverman and the discovery that one of his arms is bionic, shaking his sense of identity. It is also revealed Cybersol killed his wife and that they are preparing to send a mercenary team to Zoidstar to capture new Zoids.
Silverman had not been killed and, using the technology from the Zoid factory, was able to construct a titanic Black Zoid: a being with incredible firepower which constantly sheds an outer shell to reveal a new foe underneath. From issues 40-46, Silverman rampaged across Zoidstar, reduced to a seething hatred and desire to make Heller suffer. Zoidzilla's android pilot is destroyed; the Blue army is reduced to disarray, so the Namer takes command and has them rebuild their leader. The Black Zoid attacks and massacres the Blue forces, including the mighty Gore, and a terrified Heller fails to stop him in Gorgon. Meanwhile, Krark takes advantage of this (and of Mammoth's incompetent leadership of the Red Zoids) to form his united Zoid army.
Griff pilots Zoidzilla, almost losing his mind in the process due to a dangerous mental interface, and his firepower initially takes down the Black Zoid, only for its next inner form - armed with wings - to bring him down. At this point, Krark turns up with his alliance and a vicious air battle brings down the Black Zoid. However, Silverman emerges to attack Heller directly. The captain viciously attacks and when Silverman's body is destroyed, his head sprouts small legs (similar to the monster in The Thing (film)) and Heller has to beat it to death. One of three epilogues show one of Silverman’s arms still active and moving and the speech bubble reading "I... hate you.... Heller", suggesting he is not dead yet.
The next few issues involved the mercenaries intending to invade Zoidstar; Griff battling for control of his mind against Zoidzilla's influence and gaining amnesia; Redhorn making his return and killing Mammoth for control of the Red Zoids; the Blue Zoids rebuilding; and Krark gaining new recruits as his plans move forward. Issue 50 also revealed a strange alien lifeform was behind the Zoid Wars as part of a game, with the entire universe as "their playroom". However, the comic's cancellation with #51 meant none of these plotlines were ever followed up on.