Since I failed Sky, I obviously can't play post-game. But because I was playing the game while making the comic I had an issue where I'd plan for future events. Obviously not everything was thought out but I thought I'd be fun to share what thoughts I had for the future. c:

Brine Cave->Temporal Tower
Brine Cave would have played out the same. I planned to skip that battle already so I went with it in comic as well since it'd be very hard to create a proper experience where Gigi was brutally murdered yet was transported home. Temporal Tower on the other hand would have mirrored the game's plot more closely. Ginkgo would have been the one stopping Dusknoir. That being said, there was some thought of making Teryx the Grovyle going along but I figured Ginkgo had a good run and people would have been expecting her to appear in the third run so I figured she'd need a conclusion.
The Dialga fight was just planned to be an epic boss fight. Upon defeat the regular game plot would play out: Kiara and Gigi would walk away victorious only to have Gigi slowly fade away as she was called back to her world. Kiara would return home alone.

The Split
Gigi would then wake up in the Arcane Rift. A mysterious voice (Arceus) would give her a choice between remaining in the Pokemon world, but never to regain her past memories again or to go home to her own world and regain all her memories. Being completely split on the decision, Arceus would eventually split her into two beings. What side effects would happen because of this weren't thought out too much at this point. Human Gigi would go home and continue onto run 3 while Eevee Gigi would be returned to the Pokemon world to finish run 2.

Guild Graduation
Honestly, I was probably going to skip this and say Kiara and the gang had done this without Gigi. I probably would have shown flashbacks though or run the sequence without Gigi and have Gigi reappear at the end of the chapter. Everyone but Kiara would have evolved, Kiara would not be banned from evolving (as the game dictates) as the reasoning made no sense for me. Gigi though, would accidentally get put into a situation where she should evolve though, but she would not.

Treasure Dungeons
The team would be split into 2-3 groups and each embark into one of the treasure dungeons. This probably wouldn't effect the main story and would just be a side adventure. No one would go to the World Abyss (Kiara's greatest fear: the deepest pit in the world AND because I legitimately couldn't complete that until my party was highly leveled in my non-Nuzlocke Sky o.e). The group with Gigi (and Kiara maybe) would have gone to the Mysterious Jungle where they'd witness destruction off in the distance. Getting closer to the source they'd encounter and battle Mew and win. Though, their reason for being able to defeat Mew was not their own prowess but because Mew had just been sparring with...Mewtwo! :D Yep, this was where Mewtwo's cameo was going to be. After a little dialogue Team Sky would wander off. if Mew joined my team (s)he would have chased after them and Mewtwo would have monologued about how human-like Gigi seemed.

Sky Peak
I didn't have too many thoughts for this, only that I'd do it (being an addition to PMD:Sky) and then try to tie it into the main story (since it really is just a side adventure).

Blizzard Island
Probably would have skipped and replaced with Treasure Dungeons

Manaphy
Honestly, I had no thoughts about what I was going to do here.

Aegis Cave
Had no thoughts here as well. Might have done it because I do like Team Charm c:

Nightmares
The "Big Bad" if not mentioned before would be alluded to or hinted at now. Azurill would have fallen into a Nightmare and been unable to wake up. Gigi would reunite would Derprill but realize he was better off with Azurill's family and leave him be. Because Drowzee nearly killed Gigi and tricked Kiara into thinking Gigi was dead he was NOT going to be called in. Instead...Team ACT would appear! And Metu somehow would be the leader of it. My best thought for that was Team ACT is like a symbol, so when the old members get old they find replacements. Anyway, Gigi and Metu would have a talk and then Metu (now just known as Alakazam) would help them save Azurill.
Game events would have played out similarly. In the dream world, "Cresselia" would appear and accuse Gigi and Kiara of tampering with Time and attempt to murder them. Alakazam would then rip them out of the dream sensing something was wrong. Azurill would be saved and Gigi and her former team would split ways.

Dream Sequences
Over the next few days Gigi and Kiara would separately get death threats from "Cresselia" in their dreams. Eventually Palkia would plop in and kidnap them to the Spacial Rift. Latias and Latios would appear as cameos during this time but doing what specifically, I dunno. Again "Cresselia" and now Palkia would try to kill Gigi and Kiara for messing with Time and now Space. Though Cresselia would appear and reveal Darkrai as the antagonist.

Final Battle
Cresselia, Gigi and Kiara would engage in the final battle with Darkrai. Upon victory one of two things would happen depending on how I thought I was going to plan run 3 at that time:
1) Darkrai's memory would be wiped just as it was in-game. Though he would not make it through his escape portal. Instead he'd collapse onto the ground. Palkia and Cresselia would order his death while Kiara would agree with them. Gigi would disagree saying Darkrai could be saved and is harmless without his past memories and could maybe be good. Cresselia and eventually Kiara would agree when Gigi evolved (into either Espeon or Umbreon) based on her convictions.
2) Darkrai would have escaped through the portal but also lost him memory. Back in run 3, Human Gigi would encounter Darkrai. Having never met him, she'd still help him. He may have regained his memories eventually and chaos or internal conflict could have ensued.