- Sigma's ultimate plan throughout this crossover is to drain the energy from Mega Man and Sonic's Earths into himself to gain godlike power, but not only that, he reaches out to other worlds. And as he reaches his final stage, he announces he'll continue to outright consume world after world for further power. In other words, Sigma intended to become the Galactus of the gaming multiverse, and one who would seek to devour worlds in ambition, not necessity. For a time, he even succeeded. Good thing he never paid mind to the Chaos Emeralds.
- The first Battle Book has a scene where the Zeti control Mega Man and force him to shoot himself in the head.
- The back-up story of part four has a flashback to just before the events of Mega Man X in which Zero gives us a description of what Sigma's done:Zero: He's bombing Arcadia! The capital is burning! I've got Hunters dying in the streets to other Hunters, and he's threatened to launch nukes! There is no peace to be had!
- Sonic and Mega Man being transformed into Sonic Man and M'egga Man.
- M. Bison catches Blizzard Buffalo in the middle of installing a Unity Engine and forces him to spill the beans. Then he crushes Blizzard's throat. Complete with blood spatter.
- Alright, Sigma-2 has finally gone down! Good work, team, let's all go for milkshakes. ...Wait, wait, hold on. Sigma-3? Well, um, alright. This isn't over, but he's back to normal size. No need to panic. We've got this. —Oh. Oh, dear, did he just...one-shot Gore Magala? That's... That's quite horrible. No worries though, Ammy is on the way, and her reality-bending properties will surely— and he just no-selled the Celestial Brush. You can panic now.
- The revelation that even if the heroes can stop Sigma, it may be too late to restore all of the worlds.
- Absolutely NOTHING can stop this mess that Sigma has caused despite his defeat. He's siphoned too much energy from the combined worlds that it cooled the core of the fused planet to the point it begins imploding. The heroes try to at least contain some of the damage by trying to close the Genesis portals, but it's all in vain. Nights's Loop de Loops have no effect, Billy Hatcher can't contact the Chicken God for help, Amantersu's Celestial Brush is useless, M. Bison's Psycho power can't do a thing to the portals and the magic users find their powers no longer work. Even Sonic and Mega Man's Chaos Control can't do the job, meaning it truly is completely hopeless. The only thing everyone can do is at least try to evacuate to another world on Vyse's ship, but even then there's no guarantee it'll help or that they'll get out in time. They were mere seconds away from biting the dust...
- If that wasn't bad enough Eggman and Wily actually succeeded in taking control of the Unity engine and were more then happy to let the current reality be destroyed so they could re-write it to their whims. Thankfully Xander stepped in to prevent that from happening.
- The fact that Team Dark, G.U.N, and the Mayor of Mega City actually did die in the crossover. Many were expecting Shadow to show up to pull a Big Damn Heroes but by the end, it's made clear that that wasn't the case—he really was offed for the reminder of the story. This does result in a Heartwarming Moment though, as once the timeline is reset, Sonic immediately calls Shadow to make sure he's alright.
Nightmare Fuel / Sonic the Hedgehog/Mega Man: Worlds Unite