I've already suggested stuff for all of that!
Here's the outline I'd propose:
1: During riots, Pierce sees mind-washed sister
2: Finds out where she's being held
3: Decides to go and rescue her like the big hero he is
4: Gets caught, fails miserably. All pokemon get knocked out, so has to fight to protect them as a slayer
5: Team manages to arrive in time to save him. Unfortunately, during combat they damage some part of the facility, maybe the power generator.
6: This causes a lot of shit to happen, including Emakki getting freed.
7: Emakki goes on killing spree, while the team decides to seek out Faynoc, finish him off.
8: They fight their way through the facility, encounter signs of Faynoc's hideous experiments, as well as Enmakki's mutilated victims.
9: Big battle, Faynoc dies.
10: Pierce's criminal past is revealed.
11: Military join the fray, secure the facility
12: The brain-slaves are hidden deeper within the facility
13: The team must act quickly to save them before Enmakki finds them
14: They succeed, fight Enmakki.
15: Pierce realizes that Enmakki is his responsibility, takes up the burden
16: Everyone lives happily ever af- AhahahahaNO.
Anyway, if that's too much emphasis on Pierce (which it might be), we can make it so that he only leads from step 10 onwards. It's a public mission up until then, becomes Pierce's mission afterwards.
Whadd'ya say?
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