Issue Trinity #1
Subtitle --
Date 2003
Writer(s) Matt Wagner
Artist(s) Matt Wagner
storyline Superman saved a train full of people - a sniper had murdered the driver. After handing off to the authorities, he headed to the shooters location, but he was long gone. The shooter met up with his gang; they were taken down at their next heist, presumably by Superman, but the way they were left was not his method. While Superman visited his Fortress of Solitude, Ra's al Ghul led his team to Antarctica and released Bizarro from his icy containment.
The next day, Bruce Wayne called Clark Kent. They met; Wayne told Kent about "Purge," a criminal organization which was about to give them a lot of trouble. He'd stopped them from stealing Kryptonite.
Ra's welcomed a renegade Amazon into Purge. She called herself Diana. Slowly, he gained Bizarro's trust as he was nursed back to health. Bizarro was quested with stealing two missiles. He went a step beyond that and took an entire submarine out of the ocean. One of the missiles launched once airborne and destroyed a small island.
Superman, after learning Bizarro was loose, visited the Batcave. Batman told him about Ra's al Ghul. Later, after searching North America for Bizarro, Superman was met by Diana. She introduced herself as an Emissary and Ambassador of the Amazon people. She decided it was time to meet with him after hearing of the red-cloaked man who'd taken the sub. An awestruck Superman explained Bizarro to her, and she apologized for the implication. She offered her help in taking down the creature. They were able to track the sub's trail using her invisible jet. They found it in the Sahara Desert. They recognized the remains of a base, but it appeared to have been abandoned. Using his x-ray vision, Superman found an underground bunker. Inside, they were ambushed by suicide bombers and nerve gas. Deeper inside, they found one of the missiles, armed. Superman drilled it into the Earth, where it detonated. Before it exploded, Diana saw a crate marked Gotham City and bearing an Amazonian knot on it's rope.
She told Superman, and they headed to Gotham City.

Issue Trinity #2
Subtitle --
Date 2003
Writer(s) Matt Wagner
Artist(s) Matt Wagner
storyline Batman took down the Purge at an arms deal, but was defeated by the renegade Amazon. She split, leaving him with the weapons and survivors. As he interrogated one of them, Superman and Wonder Woman arrived. Superman had go separate them after they argued about methods, etc. Using her lasso, they got some information from the man. Superman again had to get between them after Batman broke the man's jaw. He left them saying he'd take care of the missile in "his" city.
Ra's got closer to his Amazon and she revealed to him where she was from.
Superman visited Batman in the cave. Batman told him he'd learned of a Purge plot to take out communications across the world - most all communication satellites would soon be within 5 miles of each other in orbit. A missile silo in Bulgaria had been attacked. Wonder Woman found Bizarro and followed him all the way to Ra's al Ghul. She confronted him, but was attacked by the creature. She was defeated and chained up where Bizarro once was. As the beast was about to crush her skull, Batman burst in and took him out of the equation. He rescued Diana as Ra's and his people escaped. They headed downward looking for the missile set to destroy the city.
Superman reached the launching missile. He was able to tear it apart and get the warhead into deep space before it detonated.
Batman and Wonder Woman found the missile near a Lazarus Pit. The fumes disrupted Diana's breathing, and she fell. Batman disabled the weapon; Diana was stabbed by a guard. She crawled into the pit. Superman arrived in time to see her fly away in madness.

Issue Trinity #3
Subtitle --
Date 2003
Writer(s) Matt Wagner
Artist(s) Matt Wagner
storyline Batman tracked Wonder Woman, Superman flew them to Paradise Island. Batman was overtaken by her grace and beauty - he kissed her. She punched him and sent her guards away. They formed a plan; Batman gave Wonder Woman her lasso back and left. Superman headed out to find the injured Bizarro. On his way back to the mainland in his submarine, Batman encountered what appeared to be a blond man in an orange shirt deep beneath the sea.
Artemis returned to Ra's al Ghul after being taken down by Batman. Ra's only had two missiles left. Ra's regained the Bizarro just before Superman found his trail.
After Wonder Woman told her mother what was happening, she headed back to "Man's World." Jason, in full Robin gear, headed into the cave and notified Batman they had a visitor. Wonder Woman was at the doorstep of Wayne Manor - she'd tracked him using Superman. Bruce invited her into the cave, where he clued her in that Ra's al Ghul would probably strike her homeland.
Superman found and attacked Bizarro. Ra's told him he had an attack being carried out in Metropolis. Superman flew away to save his city.
The Amazons prepared for the attack. Batman went after Bizarro while Wonder Woman attacked al Ghul. Superman joined the fight and took down some helicopters. He realized one of their own had turned against the team - it was the rogue Amazon.
Ra's was defeated by Wonder Woman and fell into the sea. Superman blasted Bizarro into a volcano and left him for dead. Batman disabled the missiles and let them sink to the bottom of the ocean. A piece of Bizarro - red and crystallized also made it's way to the bottom of the sea.
Talia found and recovered her father's body.

hardcover edition trade paperback edition

Notes, references to time, and chronology:
Wonder Woman met Superman and Batman for the first time.
Wonder Woman was forced to use the Lazarus Pit under Gotham City.
  This was a great starting point for Wonder Woman in the post-CoIE DCU. However, post-Infinite Crisis, she existed previous to the original Crisis and was a founding member of the JLA. I'm placing it here, though the events may or may not be canon.