The manga starts off just before Operation Meteor with Duo wiping out the Alliance Space Forces 304th Leo Team.
On Earth, Lady Une informs Treize of this. He guesses it's Operation Meteor and the unidentified suit is Gundam. He tells Une to relay the information to Zechs in space
Proffesor G picks up Duo in a transport ship. As they're being pursued by an OZ ship from Barge, G decides they head for Colony V08744 (the same colony we see Duo on in his Episode Zero story) and that they join the Barton Foundation to carry out Operation Meteor as it was originally intended. Duo says he'd rather die than be forced to take part in massacre.
The next scene is in Colony V08744. Just like his flashback from Endless Waltz, Duo places explosives on Deathscythe. He then reminsces about his experiences on the colony before he attempts to blow up his Gundam.
The conversation between him and G goes the same and we see Duo "stealing" Deathscythe. G briefs him on his first mission and Duo launches.
From his shuttle, Duo actually sees Heero on his way to Earth, as well as Zechs's shuttle. Heero ditches the rentry capsule and Zechs deploys in his suit, now retconned to a white Leo prototype called a Grief).
The brief battle plays out just as it did in Episode 1, with Wing Gundam ending up at the bottom of the ocean.
Duo, Trowa, Quatre and Wufei all go through their first missions in the exact same way. Zechs shows Otto and the nameless co-pilot pictures of the Gundams.
Relena is seen approaching Heero with an invitation in hand.
The search for Wing Gundam begins and Duo destroys a bunch of Alliance Cancers with Zechs nearby. Duo destroys the carrier and Heero finds missiles to destroy Wing Gundam using a school's computer.
The OZ search party finally finds the Gundam only for Duo to wipe them all out. Heero (now in classic vest and spandex shorts attire) walks away from two knocked out guards in a base.
There's a splash shot of everything Relena has experienced up till the moment she tracks down Heero at the base: Their first meeting on the beach. Seeing him enter her class. Her meeting with Zechs in Episode Zero, where he described himself as a "Little Prince" (as seen in Episode Zero)
. Heero tearing up her invitation, wiping her tear and uttering that
In the present, he aims a gun at her, Duo shows up and things go the same way as the series.
Heero is held in the Alliance medical building and unconsciously reminisces about the orders he got from Doctor J at the start of OM, and them deciding on a codename (the same flashback he has in Episode 31). He wakes up and immediately realizes where he is. Eleswhere in the building, Duo observes Relena's car pulling up to the medical building from a video surveillence room and wonders what she's doing there. He muses about the "broken cart" (code for his Gundam) being recovered and then leaves for another room.
The rest of the scene goes exactly as it did in Episode 3, ending with Heero and Duo on a beach about to be picked up by Howard.
Trowa joins the circus, Quatre takes in the Earth's beauty and Wufei purchases some explosives and a truck.
Switch to Howard on his crane ship at night looking at the moon. He then has a flashback to when he and Doctor J stashed Peacemillion underneath a crater on the moon. Episode Zero features the same scene, except it features Prof. G instead of Doc. J.
The flashback ends and Duo recovers Wing Gundam while Heero tends to his thigh bone.
The manga stays with them as Heero does diagnostic checks on his Gundam while talking with Duo. Howard looks down on them from catwalk. After Heero says he doesn't want anyone touching his mobile suit, Howard has another flashback, this time to AC 183 when he was working as an Alliance MS developer at the Corsica base. A young Treize says the Tallgeese will eventually be his. Because he felt it was a suit befitting a hero, he asked Howard to paint it an elegant color. In the present, Howard muses to himself that white (the same primary color as the Gundams) was acually a "foolish" color.
At Treize's estate, Zechs advices him through a video monitor for OZ to make a move at Corsica. Trowa is en route to Corsica on a boat with Heavyarms under wraps, while Quatre and the Maganacs load up their suits on transport planes.
There's a brief narration on the Specials just like in Episode 3.
Zechs arrives at the base and is introduced to the Tallgeese by Walker.Commander Bonaparte curses the Specials as he prepares his to take off in his zeppelin despite a possible attack from the Gundams. Trowa starts his attack with Heavyarms. In much more epic fashion than the anime, he uses Heavyarms to blasts part of the base with a space laser mounted on a truck, leveling a building and a bunch of Leos. He then heads for the base to continue the attack.
The next scene is back at Treize's estate. While on his laptop, he summons Une and asks her to call in several engineers, one of them being Oswald Walker of the Specials. He looks at blueprints of Epyon and says they must also acquire Gundanium alloy because the "next machine for the new era" is necessary. He then makes a comment about miracles being created while looking over blueprints to Tallgeese II and III.
Switch to Wufei driving the truck he previously bought with Shenlong on the back. An encypted message on a monitor by his side tells him of others attacking OZ facilities. He figures it must be the Barton Foundation's people and says he'll kill them if he comes across them.
At the St. Michael Institution (St. Gabriel in the anime), Relena overhears two girls talking about how no one has seen Heero in a while.
Heero works on Wing Gundam on Howard's Craneship with Deathscythe laying beside it. A mission briefing comes through telling him to destroy an OZ transport ship carrying Gundanium (more than likely for Treize). Duo questions him being able to carry out the mission considering the state of his Gundam. He then thinks to himself that he and Heero must be allies based on how their missions have no room for failure.
We then see Trowa continuing his attack. Coincidentally, he says his missions have no room for failure and that when he runs out of bullets, he'll run out of life.
Walker and his Specials comrades launch in their Aries suits while Zechs looks on. Just like the series, Commander Bonaparte orders his troops to surround and destroy Heavyarms. Also sticking to the anime, Trowa acknowledges the plan was right in theory but that Bonaparte should have considered the enemy's potential before giving the order. He drops the Gundams tank-like treads, start rolling forward and unleashes the suit's firepower in full.
Bonaparte is stunned and Walker delivers his orders for "soldiers of the future".
Back in the base, Otto tells Zechs the Tallgeese has been loaded and that Bonaparte got away safely. He then says he wants to fight the Gundam in a Leo but Zechs says he'll need his help protecting the Tallgeese.
Trowa takes out a bunch of Leos before running out ammo. An Aries charges at him and is detroyed by a Maganac suit. The entire corps starts firing on the base, with Sandrock behind them.