* CreatorBreakdown: A literal example, for according to [[http://bumbleking.com/forum/viewtopic.php?f=6&t=6767&start=27 this]], Jamal Peppers, who drew parts one through three and most of four, was hospitalized before he could finish the last few pages of part four. Ryan Jampole stepped in to finish the pages for him so things could go according to plan.
* DevelopmentGag: In Sonic Universe #51, Doctor Light is seen working on Bond Man, who he's "been putting off building since the original line."
** In the Off-Panel comic for Sonic Universe #54, Bass announces that he and Metal Sonic will combine their power, resulting in... a musical act. Mega Man thought they were going to fuse together. This joke is based on an idea of [[FusionDance Metal Sonic and Bass were originally going to fuse together into one being]], but Sega rejected this idea.
* ExecutiveMeddling: A rare case where a crossover is used to ''execute'' the meddling. Namely, [[spoiler:all of the ''Sonic'' characters created by other writers pre-''Sonic'' #160 or associated too strongly with them can't be used anymore. So the CosmicRetcon at the end doubles as a way to get them out without requiring another story or just killing them all off.]]
* ExecutiveVeto: Sega outright refused an idea where Metal Sonic and Bass would fuse together during the climax, despite allowing other fusions of Mega Man and Sonic enemies like Chaos Devil.
* InspirationForTheWork: This comic, alongside [[ComicBook/SonicTheHedgehogMegaManWorldsUnite the sequel]], inspired Jun Sunoue to create the “Mega Man 4 Medley” in ''VideoGame/SuperSmashBrosUltimate'', which was Mega Man’s music done in Sonic’s signature sound.
* KeepCirculatingTheTapes: A consequence of Archie losing the ''Sonic'' license to IDW, this crossover cannot be reprinted, and due to Sega and IDW wanting to move on from the ''Archie Sonic'' material as of this writing, it looks pretty unlikely it'll get reprinted at all.
* MilestoneCelebration: As the 250th issue of Sonic the Hedgehog, Part 9 primarily features a Big Badass Battle Sequence so massive that Ian Flynn described it as something along the line of "the moment I'll get death threats from the art team." It shows. Also, it includes a reprint of the ending of Sonic the Hedgehog #229, the end of the first usage of the Genesis Wave. The "Off Panel" comic is all about the milestone, for good measure.
** Then there's the fact that Part 4 was the 25th issue of Mega Man and immediately prior to the crossover was the 50th issue of Sonic Universe that introduced the version of Metal Sonic that would show up in the crossover. Milestone celebrations all around!
* ShoutOut: Sonic states that Vector Man's name reminds him of [[VideoGame/VectorMan a trash collector]].
* WhatCouldHaveBeen: Ian Flynn was originally planning to have Bass and Metal Sonic combine into a single entity, but this idea was shot down early on. The weakness of said boss would've been Rouge Woman's Black Wave, the only time it would've been used.
** According to Spaz in the first paperback's special features, the basic idea of having ''Archie Sonic'' crossing over with ''Mega Man'' dates as far back as when ''ComicBook/MegaManDreamwave'' was running, but the deal never went through. Not much is known about this version of the crossover, though Spaz said all that really got carried over to the final version was the basic idea of a "sneakers and helmet" image that got used in one of the teasers.
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