Note that depending on availability and stuff, none of these stuff will actually happen in-RP as in in posts, but in case I can't make them happen I'll leave them established as canon via Word of God in the wiki, or here in this very post.
RtAU (alt?):
* Silent will be offshore somewhere during the attacks and he will be returning to PEFE HQ offscreen.
* Ichtacya and her two colleagues (Foreign!mence and Foreign!goose) will be hired or recruited by the Angela Resistance, and assist them in raiding draconic forces supplies; after a series of successful hits, they are forced to stay behind to give some Blitz Evacuees some time and are surrounded / captured. Ideally her fate will be different than what PMD-B records.
* Ichtacya×Chilliwack OTP?
* Sometime during the raids Ichtacya's trio will probably/hopefully face one of the Seven Jerk Dragons or their forces, and manage to damage him/her enough so as to meaningfully contribute to their eventual defeat when the player characters battle or chase the Seven (say, cutting an eye or nearly dislogging an arm or leg)
* Pokéteco will have a moment of glory by helping the PEFE HQ personnel escape away from the invading dragons, of course via INSTA-DEAFFFF!!!
* Silent and Maekrite will very likely travel to Unova together with Teala. That's where Guardianshipping actually will become canon.
* Silent will send Venomoth and Magneton back to his origin noncanon land to assist the resistance there.
* Cinder will be called to serve the Goldenrod army (as he was granted the position of General during the AU) and if accepted he will lead the local resistance in an effort to spread to Violet and Azalea.
* After being offscreen for long enough training under the mentorship of one of the Johto Gerbils, Inka will return to Johto to help cleanse it of the draconic invasion.
* A group of forest mons (likely the Umbreon and Espeon of the SWAT team) will be sent to escort and protect Icelus to help gather allies against the invasion.
* Vinollo and Rize will be sent to two Johto locales (Alto Mare and ????) to lead the resistances there, as homages to Assassin's Creed.
* Silent will probably try to reestablish some technology in Unova before leaving to the neighbour regions with Maekrite. Probably headed to Orre.
* With Johto probably almost overrun by the dragons, the Nidoran Colony will issue an ultimatum to Blackthorn (who have sided with the invaders) to abandon Johto for High Treason or fight to death, which will be ignored. A force of Pokémon will go raid the city in an unsuccessful effort.
* Inka will make her General Tao entrance as a warning shot and challenge the dragon leaders there to a battle; in a 1-vs-many battle royale Inka will kill all of the draconic leaders in the area, then the remaining dragons will accept the ultimatum. The 'zards from Charizific Valley will probably be the ones assigned to police the place.
* Because of the events in Blackthorne Inka has to be expelled from the Goldenrod Colony. She goes live to either PEFE HQ or Silent's region with Baluarkos.
* Shortly after the invasions end, Roa will have her first litter, to give closure to the pairing.
PEFE Exploration:
* Aamu (Maekrite's rival Nidorino) will return to the colony for a season and try to one-up Maekrite with his girlfriend.
* Only current plan actually within the PEFE locale is that Algira, Lileep and Python will be left available for RCing for exploration, fun and shipping purposes. Silent will be explicitly away on the field somewhere.
* If Tagg wants to work on Helios×Algira somehow, that will give closure to the pairing.
* Harriet and Copahue will decide that they want to have their own egg, giving closure to the pairing.
Holon/Conquest:
* Depending on when does the arc take place IRL, the reveal of what morph Silent's ????eon is might happen there.
* Sol will likely want to travel to Holon because of science and knowledge, so if she goes she has to tag along with someone.
* Ichtacya will request to leave the team and returned to the wild.
* Two old foes will reappear. Can't reveal more due to spoilers.
More plans are pending.
“Thou hast forgotten the face of thy Lord. Remember, mortal, and fear pet me.”