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Digimon Chronicle is not a manga, but rather the storylines of the new Pendulum X devices. It seems that there never was any source stating that Digimon Chronicle was a manga, but that it was simply something that people had jumped to conclusions about. There were little manga strips sold with the Pendulums, about six pages each, but nothing more. This is what happened in each Pendulum.
Pendulum X 1.0
Since Digimon who had X-Evolved could not be deleted by the X Program, Yggdrasil ordered compulsory deletion of the X-Evolution Digimon and sends the Royal Knights to do the job. The X Digimon are overwhelmed by their power, and the extinction of X Digimon seems likely. However, DORUmon fought bravely with his Tamer, Kouta, and eventually evolved to DORUghoramon who was able to battle and win against Omegamon, one of the Royal Knights!
But even if he had to become an X Digimon, Omegamon had to complete his mission. He X-Evolved to Omegamon X and DORUghoramon was beaten away at last.
Darkness wrapped around the fallen DORUghoramon, and although he was on his deathbed, the X Antibody forced him to evolved once more...it was called the X-Evolution of death. He evolved into Death-X-DORUghoramon, his flesh consumed by the evolution...
Pendulum X 2.0
Yuuji and Ryuudamon also battle one of the Royal Knights, in this case Dukemon. Ryuudamon has evolved to Ou Ryuumon, and so it is that Dukemon is defeated and X-Evolves just as Omegamon did...
Pendulum X 3.0
The management system of the New Digimon World remove and transmitted the life data of DORUmon from Death-X-DORUghoramon. However, the remaining data still survived as Death-X-mon, and appeared in the Future Digital World, Skuld. Because he doesn't have a Digi-Core - which is life - he is extremely difficult to kill. Ordered to eliminate the X Antibody immediately and decisively, the Royal Knights arrive in Skuld and battle Death-X-mon. Omegamon uses the OmegGainForce, and although he lets out all of the 'DELETE' power, he is unable to delete Death-X-mon.
Meanwhile, DORUmon evolves to Raptordramon, Grademon, and finally Alphamon! Because both Ou Ryuumon and Alphamon need more power to defeat Death-X-mon, they transcend space-time and evolve into Alphamon Ultimate War Blade King Dragon (form) and fight Death-X-mon in the last decisive battle...!
And yes, of course they won. Apparently, after the battle, some sort of compromise with Yggdrasil is made. The Digimon seem to survive, but a new program - the X Eraser - appears, and so the X Digimon return to normal.