Executive Meddling: The story was likely meant to conclude in the magazine's 50th issue, but due to the magazine's apparent need to print the Comic Book Adaptation of The Lion King (which itself was already being printed in a Marvel Comics graphic novel), there was a two-issue gap between Chapters 1 & 2, and the last installment came one issue later.
Perhaps this wasn't such a bad thing though, as the issue it ended up concluding in was editor-in-chief Tommi Lewis's final issue of Disney Adventures and it seems a fitting tribute to the end of an era for DA to have such a story end there.
Also, when Solego blows up the Gizmoduck armor, the artwork depicting Fenton flying away seems to have been hurriedly added in at the last minute; it just doesn't look quite right compared to the rest of the panel, and Solego comments that he's been disintegrated. It seems like he was intended to be killed outright and then revived at the end of the story, instead of simply teleported back into the armor.
Keep Circulating the Tapes: To date, The Legend of the Chaos God has never been reprinted or made available anywhere outside of its original printing. One can only hope that since Marvel and Disney have now become a single entity, or since Boom! Kids is reprinting some of the DuckTales stories, it might eventually be reprinted in its entirety.