The fact is, the "evil/antagonistic" chunk of the empire isn't overly large, its just that they are near the top and nearly unopposed in military command due to the way they are holding the reins.
Thing is, this means that, as one would expect of high-ranking officers, they'd have a large number of bodies under their command, due to the hierarchical structure that would exist (All the way down to the grunts, and something tells me that after the initial Guardian conflict, they'd have been revising their forces for the eventuality of another opponent with anti-dissonance capabilities. Combined-arms tactics, so to speak.). As for revealing themselves and 'going for the gold'...Gier I could see there (If he doesn't eat it either to the PCs or Zorn. Seeing a 1/3 chance for the eventuality of any of those three happening). Not sure if Zorn would do something that stupid, however, and Sigkeit's at least capable of listening to reason. If they have a superior between them and the military leader...hard to say if he's that stupid either.
Anyway, enough of that point.
Encounter/Boss possibilities by chapter, starting with Mirek 2
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Mirek 2:
Encounter: Wilderness section(s)?
Isolde 4:
Encounter: Wilderness section
Boss: Assassins. Possibly give them some names. Alternatively, keep them alive for a case of Chekhov's Gun later on( muuuuuch later )
Possible encounter: Thug(s) who don't like the poking for info.
Noemi 5:
Encounter: Wilderness section, Disquieted Area.
Boss: Disquieted Abomination
Boss: Possible thing to do with Erastus' past.
Mirek 3:
Boss: Guardian Commander Orianna
Isolde 5:
Encounter series: Disquieted beasts, Guardian party
Boss: Guardian Commander Val
Noemi 6:
Encounter series: Disquieted beasts.
Boss: Disquieted Abomination?
Boss: Guardian Commander Seraphin
Mirek 4:
Boss: Yiu 2
Isolde 6:
Random encounter area: Wilderness section
Encounters: Varied assassins/hired help.
Boss: Selena, with imperial support squad.
Noemi 7:
Encounter areas: Wilderness, old Guardian base
Mirek 5:
Encounter strings: Guardians
Noemi 8:
Boss: Yiu 3
Isolde 7:
Encounter area: Wilderness.
Mirek 6:
Encounters/Encounter area: Guardians, Disquieted beasts
Boss: Guardian commander? (One-shot)
Noemi 9:
Encounter area: wilderness
Pathsplit decided at the end of the chapter, presumably. If scores for both sides are similar, player actively chooses which side.
{Guardian Path}Attack:
Encounters: Imperial Military, Guardians
Boss?: Military commander Reinhild
Noemi 10:
Encounter area: Disquieted area, Wilderness areas
Boss: Yiu 4
Encounter area: God-Kings' Island(Soulless, Imperial Soldiers, Guardians)
Boss: Military commander Gier
Encounters: Imperial Soldiers
Boss?: Military leader
Isolde 8:
Encounter area: Guardians, Soulless
Boss?: Military commander Sigkeit
Boss: Selena 2[with Flow Amplifier]
Mirek 8:
Encounter area: Imperial soldiers, Soulless
<<TIMESKIP GOES HERE>>
Noemi 11:
No encounters. Can possibly explore GK Island area.
Yiu 1:
Encounter(s?): Guardians
Isolde 9:
Encounters: Guardians
Boss?: Guardian commander (One-shot)
Mirek 9:
Encounter/Encounter Area: Soulless
Yiu 2:
Possibly no new areas.
Noemi 12:
Possibly no new areas.
Isolde 10:
No new encounters or areas. Optional stuff is probably available around now to relevant PCs.
Mirek 10:
Encounters: Soulless
The Hunt:
Encounter area: Soulless
Noemi 13:
No new areas.
The War:
Possible strategy-battle minigame. Alternatively, encounters: Guardians
Boss:Guardian commander Val.
The Strike:
Boss: Guardian Commander Orianna
Encounter area: Guardians' HQ
Boss: Guardian Commander Seraphin
Boss: Guardian Leader
{end Guardian Path. go to The Call}{Imperial Path}Attack:
Encounters: Imperial Military, Guardians
Boss?: Guardian Commander Val
Noemi 10:
Encounter area: Disquieted area, Wilderness areas
Boss: Yiu 4
Encounter area: God-Kings' Island(Soulless, Imperial Soldiers, Guardians)
Encounters: Guardians
Boss: Guardian Commander Seraphin
Boss: Guardian Leader
Isolde 8:
Encounter area: Guardians, Soulless
Boss: Selena 2[with Flow Amplifier]
Mirek 8:
Encounter area: Imperial soldiers, Soulless
Boss: Guardian Commander Cecilie
<<TIMESKIP GOES HERE>>
Noemi 11:
No encounters. Can possibly explore GK Island area.
Yiu 1:
Encounter(s?): Imperials, Imperial Supersoldiers
Isolde 9:
Encounters: Imperials, Imperial Supersoldiers
Boss?: Imperial Commander (one-shot)
Mirek 9:
Encounter/Encounter Area: Soulless
Yiu 2:
Possibly no new areas.
Noemi 12:
Possibly no new areas.
Isolde 10:
No new encounters or areas. Optional stuff is probably available around now to relevant PCs.
Mirek 10:
Encounters: Soulless
The Hunt:
Encounter area: Soulless
Noemi 13:
No new areas.
The War:
Possible strategy-battle minigame. Alternatively, encounters: Imperials, Imperial Supersoldiers
Boss:Imperial Commander Sigkeit
The Strike:
Boss: Imperial Commander Gier
Encounter area: Imperial HQ
Boss: Imperial Commander Reinhild
Encounter area: more Imperial HQ
Boss: Military Leader
{End Imperial Path.}The Call:
No new areas. This is when the last sidequest stuff should probably be done.
The Desert of Red Glass:
Encounter area: self-explanatory. Disquieted abominations on par with the Soulless, possibly nastier.
Phantasm Fortress:
Encounter area: Phantasm Fortress (Initial area)
[[Parties split here. Each of the mains must form a party with the members available]]
[Noemi Section]
Encounter Section: Phantasm Fortress(Central Branch) (Randoms' intensity is under given conditions)
Boss:?? (Skipped under given conditions)
Boss:?? (Support dependent on conditions)
[Mirek Section]
Encounter Section: Phantasm Fortress(West Branch) (Randoms' intensity is under given conditions)
Boss:?? (Skipped under given conditions)
Boss:?? (Support dependent on conditions)
[Isolde Section]
Encounter Section: Phantasm Fortress(East Branch) (Randoms' intensity is under given conditions)
Boss:?? (Skipped under given conditions[Selena recruited])
Boss:?? (Support dependent on conditions)
[Merge]
Encounter area: Phantasm Fortress, Final corridor
Boss: Erastus' ultimate summon. Whatever it is. On steroids.
Final Boss: Erastus
The End:
Encounter: LONG CUTSCENE. CANNOT BE ATTACKED. YOU MUST WATCH IT.