Okay, fiddling around with the Vargas script... I fixed it! (I think) Have a look.
FC 14 00 00 ; If VAR000 has all the following bit set: 0
FC 15 00 04 ; If VAR000 has all the following bit cleared: 4
FC 09 05 08 ; If target Sabin (all allies if N/A) is not affected by status Condemned
EF ; Special
F3 12 00 ; Text: " I tire of this!<D> "
F9 01 00 04 ; VAR000 set bit: 4
FE ; End If and reset targeting
FC 14 00 04 ; If VAR000 has all the following bit set: 4
FC 15 00 02 ; If VAR000 has all the following bit cleared: 2
FC 08 05 08 ; If target Sabin (all allies if N/A) is affected by status Condemned
F9 01 00 02 ; VAR000 set bit: 2
F3 43 00 ; Text: " There's no going back!<D> "
FE ; End If and reset targeting
FC 0B 32 00 ; If timer has reached/passed 50 (locks timer)
FB 00 00 ; has battle timer set to 0
F3 0A 00 ; Text: " Come on.<D> What's the matter?<D>"
EE ; Battle
EE ; Battle
FE ; End If and reset targeting
EE ; Battle
FD ; Wait until the attack sequence is called upon again, then continue (reset targeting)
F0 E6 E6 E6 ; Rand. spell: Gale Cut or Gale Cut or Gale Cut
FD ; Wait until the attack sequence is called upon again, then continue (reset targeting)
EE ; Battle
FF ; End first wave of attack
FC 12 00 00 ; If following monster is/are dead:
F5 0C 01 FF ; Monsters #1, #2, #3, #4, #5, #6 are killed, dies like a boss
FE ; End If and reset targeting
FC 02 5D 5D ; If monster has been attacked by spell: Pummel or Pummel, will target attacker
F7 09 ; Trigger event: conclusion of Sabin & Vargas
F5 0B 01 FF ; Monsters #1, #2, #3, #4, #5, #6 are killed, diagonal
FE ; End If and reset targeting
FC 15 00 00 ; If VAR000 has all the following bit cleared: 0
FC 05 00 00 ; If monster has been attacked
FC 06 36 55 ; If target self has less or equal than 10880 HP
F9 01 00 00 ; VAR000 set bit: 0
F3 42 00 ; Text: " Off with ya now!<D> "
F7 07 ; Trigger event: Sabin intro defy Vargas
FE ; End If and reset targeting
FC 14 00 00 ; If VAR000 has all the following bit set: 0
FC 05 00 00 ; If monster has been attacked
FC 15 00 01 ; If VAR000 has all the following bit cleared: 1
FC 06 36 51 ; If target self has less or equal than 10368 HP
F7 08 ; Trigger event: Sabin must use blitz (instructions follows)
F9 01 00 01 ; VAR000 set bit: 1
FE ; End If and reset targeting
FF ; End
Amazing! May be bugs involved. Have to continue to investigate.
EDIT: I bolded the relevant bits for you all. I tested a few times and I have not found any bugs in this code yet.