I had started a write-up for this issue earlier--it is one of my favorites on this list--but I could just say "It's Walt Simonson, it's awesome!" and call it good. From 2002, Orion #25, "Children of the Pact!" Written and penciled by Walter Simonson, inks by Bob Wiacek. (I don't usually note them here, but letters by the awesome John Workman, colors by Tatjana Wood.)
For those of you not up on your New Gods theology, Scott and Orion have a weird family dynamic: Highfather of New Genesis and Darkseid of Apokolips entered into a pact where they traded sons, the theory being that each having the other's son would guarantee peace. Darkseid was probably two steps ahead of the game, though: Orion has his dad's temper, and would have a hard time fitting in; while Scott was given to Granny Goodness and her orphanage boot camp and basically tortured for years until he escaped, breaking the pact. On the other hand, Scott ended up married to Big Barda, so maybe he did get the better end of the deal.
Now, here comes a somewhat game-breaking revelation: Scott has the Anti-Life Equation. In fact, he's always had it, since his days on Apokolips: after sneaking out of Granny Goodness's barracks one night, young Scott witnesses a massacre, Darkseid's dog soldiers attacking a slum of the wretched Hunger Dogs. Not knowing his power, Scott accidentally unleashes the Equation, first making the soldiers attack each other, then inadvertantly killing them all, soldier and peasant alike. Disraught, Scott clamps the Equation down, burying its power inside him.
I always felt like that's kind of a big retcon, and that it pretty much breaks Mr. Miracle as a character for further use; but it does add a lot of wrinkles that are interesting. Along with the implication that Highfather as much as gave Darkseid the Anti-Life Equation he'd been searching everywhere for; Scott, a character all about freedom, was now metaphorically shackled by guilt and responsibility. Moreover, Scott wonders how much his dad Highfather knew: did he know, and send Scott to Apokolips for training, seasoning he couldn't get on New Genesis, or as a weapon?
Still, I'm not sure this was ever brought up again; and it's at least a reboot or two back now. The rest of the issue is Orion getting his groove back: Scott is injured by a Parademon attack, on the day he takes flowers to the massacre site on Apokolips. (The Parademons weren't sent by Darkseid, though, but by Metron, who had some suspicions.) Disguised as Mr. Miracle, Orion takes the flowers, but this year Darkseid and Apokolips are waiting: Orion gives a pretty fair showing as Miracle, but then brings the pain when he reveals himself. "You, who were so bold when you thought you'd caged a tabby cat!" He demolishes a good chunk of Apokolips, before leaving the flowers in remembrance, and challenging his father anew.
Meanwhile, back on earth, Metron confronts Scott, having figured it out. Orion overhears and considers simply murdering Metron (who's often portrayed as nicer, but is somewhat ruthless in his pursuit of knowledge) but instead uses Darkseid's "temporal bender" to go back in time and erase the clues Metron found, leaving him in the dark...and altering the timeline so Orion's disguised visit to Apokolips didn't happen, but that's OK. He knows what he needs to do, now; and is grateful for his brother Scott's help.
Easily my favorite story with either Orion or Mr. Miracle. Orion has had a bit of a minor resurgence in the New 52, appearing in Wonder Woman and getting a sharp-looking new figure out of the deal.