- "I cannot let you win. I gave the Bat a fighting chance, but he was not strong enough. If man won't kill God, the Devil will do it! An ancient Kryptonian deformity; blood of my blood, born to destroy you!... Your Doomsday."
- ―Lex Luthor to Superman[src]
The showdown in Gotham Port was a battle that occurred between Superman, Batman and Wonder Woman and the United States Armed Forces, against Doomsday, a genetically mutated Kryptonian creation of Lex Luthor. This battle concluded with Doomsday and Superman facing off in a fierce brawl that ended with both Kryptonians dead at the other's hand.
Lex Luthor, through political manipulation, was given full access to the Kryptonian scout ship, as well as the cadaver of General Zod. He peeled off Zod's fingerprints using a shard of kryptonite, placing them on to his own hand, to which he then used to unlock the ship, using Zod's DNA credentials for unrestricted access to the ship's Genesis Chamber. Lex then placed Zod's body into the Chamber's pool, where he then introduced his own DNA to the Chamber. After commanding the ship's A.I. to repair the body, Luthor was warned that the genetic abomination he was attempting to create had been outlawed by the Council for generations. Lex, however, merely asked the A.I. where the Council was, to which it replied that it was disbanded, and demanded the procedure continue. It began working, eventually hatching a sac, revealing Doomsday.
Superman arrives at the Scout Ship 0344, where Lex Luthor is waiting for him. Luthor taunts Superman for being unable to defeat Batman in order to save his mother when he is then called by Batman informing him that Martha Kent is safe. Luthor furiously refuses to accept defeat, claiming that if “Man won’t kill God, the Devil will do it.” Luthor reveals what he has been working on to destroy Superman, dubbing it his “Doomsday.” Doomsday emerges from his sack and attempts to attack Luthor, but is stopped by Superman. Doomsday grabs Superman and then brings him outside of the fortress and crashes into Heroes Park. Doomsday throws Superman through the Superman Statue and then proceeds to rampage across the city. Doomsday lands atop Lexcorp tower where he is confronted by military aircrafts.
The military open fire, causing Doomsday to release a burst of energy, destroying the aircrafts and surrounding buildings. Superman re-enters the fight and begins to bring Doomsday further up into the atmosphere. As the military observes, they decide to launch a nuke at the two. Upon seeing the nuke, Superman punches Doomsday further and further into space, before finally holding him in place to be hit with the nuke.
Arrival of Wonder Woman
- "Is she with you?"
"I thought she was with you."
- ―Superman and Batman[src]
Doomsday plummets back to earth and crash lands on Stryker's Island. As he rises, he begins to adapt as more bones begin to protrude from his body. He release another, much stronger burst of energy. He is spotted by Batman, who realizes the only way to kill Doomsday is with the kryptonite spear that was left in Gotham City. Batman leads Doomsday to Gotham, but has his Batwing damaged, making him an open target for the monster. Meanwhile, as Superman's horribly weakened body is exposed to the sun, he begins to quickly recover. Back at Gotham, Doomsday shoots his heat vision at a cornered Batman, however the rays are deflected by Wonder Woman, knocks the monster back. Recovered himself, Superman then charges at Doomsday yet again, sending the beast flying into a chemical silo, causing an chain reaction explosion. After seeing the creature in action, Lois Lane realizes she needs to retrieve the kryptonite spear she had thrown into a deep pool and rushes back to the pool to find it. As Doomsday rises once again, Batman, Superman, and Wonder Woman stand ready.
The death of Superman
Doomsday unleashes another blast, resulting in the building Lois Lane had been in collapsing, trapping her in the pool. Superman and Wonder Woman then proceed to attack Doomsday in tandem, while Batman tries to expose the monster to the kryptonite gas. However, Doomsday manages to overpower the heroes whenever they attempt to take him on one on one. Superman then hears Lois drowning and rushes to save her and retrieves the kryptonite spear, while Wonder Woman and Batman attempt to keep Doomsday distracted, however, it becomes clear that they won't be able to keep him distracted for long. Wonder Woman manages to cut off the creature's arm, however, it only results in a sharp skeletal protrusion growing back in its place.
Superman sees that the only way to stop Doomsday is for him to stab Doomsday, which would make him more vulnerable in the process. As Wonder Woman manages to temporarily restrain Doomsday with her lasso and Batman weakens the monster with his last kryptonite grenade, Superman charges at the creature, being exposed to the Kryptonite himself, and stabs Doomsday in the chest with the kryptonite Spear. The spear, however, does not manage to fully pierce Doomsday. Wonder Woman then loses her footing, allowing Doomsday to pierce Superman's chest with the bone protrusion on his arm. A mortally wounded Superman uses his last reserves of strength to further impale Doomsday and manages to fully push it through the other side, finally killing the creature, as the mortally wounded Doomsday managed to fatally stab right through Superman's otherwise invulnerable chest with its tremendously sharp arm bone protrusion. A huge massive yellow and green light bursts out of Doomsday and the beast collapses to the ground dead with Superman screaming before he succumbs to his wounds and dies as well.
Bruce, Diana, and Lois Lane attend the funeral of Clark Kent in Smallville (with Bruce himself paying for it, as an anonymous donor), along with Pete Ross, Lana Lang, and Father Daniel Leone, who presides over it.
Bruce and Diana remain at the cemetery afterwards, and Bruce, guilt-ridden over having "failed [Superman] in life" (mainly due to Bruce's horrible actions against Superman, and due to Bruce having wasted 2 kryptonite gas grenades on him, while they might have instead been used to kill Doomsday without losing Superman), asks her to help him honor Superman's heroic sacrifice by helping him bring together the three Metahumans from Lex Luthor's file (Flash, Aquaman, and Cyborg), in case a threat of that scale ever should arise again. Diana inquires why Bruce is proposing it. He replies that it is simply due to a feeling he has that things will imminently get worse (in reality, he was following the instructions given to him by the scarlet time-traveler that appeared in one of his "dreams", as well as heeding Lex Luthor's enigmatic warning).