Ok, here we go. I'm posting as much as I know about the plots I am involved in, in the hopes that it helps whatever issue is going on. Anyone involved in these, feel free to contribute.
The Fillydelphia mission - Iron, Zezoor, Tack, and a team of NPC performers being puppeted by mega along with Iron's team of NPC SEAPony operatives have landed in the city and are attempting to lure the elder there to see a 'performance'. The performance itself is a diversion to enable Iron, Tack, and the SEAPonies to maneuver themselves into position to kill it. This mostly involves Zezoor's team putting on a good show, and Iron's team setting up traps around the audience and/or using weapons disguised as part of the show to catch the Alliance off guard.
Griffon Hunger Games - a tournament in Clawdor that any griffon- and his/her second- is allowed to enter into is about to get under way. In my headcanon to avoid killing off PC characters, the tournament rules allow someone to surrender and thus remove themselves from competition, since surrendering is a sign of weakness and all. typically, most griffons would rather die than surrender, so most of the fighting will be to the death- with the overall victor getting to challenge the current Kaiser of the Griffon people as a whole for leadership of the entire race. A group of anti-Alliance operatives- so far consisting of Razorclaw, Flame Mane, Archer, Archimedes, a puppeted Mikael, and possibly Boreas are entering the tournament in order to unseat the Alliance-friendly Kaiser and switch the griffons to the Equestrian side of the war. Phase 1 of the overall plan is to take out the most cut-throat and/or alliance-friendly competitors prior to the tournament's start. Unbeknownst to the Equestrian team, Mauti and Tide are already in Clawdor, and have a similar plan to narrow down the competition. During the tournament itself, the Equestrian team is relying on using the MAGIC OF FRIENDSHIP- i.e. team-based tactics (using Archer to snipe competitors, Arc designing weapons that can be smuggled in, Flame using his magic to help the fighters in the arena)- to give them an edge over the power-hungry, ambitious, selfish sort of griffons the Grand Tournament usually attracts.
The School - Val is building thermite weapons, which would be kind of like pony-versions of nukes: indiscriminate, brutal, and ugly weapons that destroy pretty much everything they touch. I'm hoping for a crisis of conscience at some point, but that's for Future Captain to figure out.