i have yet to work out my dearest beloved anon HOWEVER it's one of those things where father alexander leads a group similar to how sonya does. he sees alex as a martyr of sorts for like, all that is wrong with the city and how the city has imposed its will onto him and sees him more as an example to be saved rather than a person, while alex just thinks he's a general nuisance but still grateful for his sympathy from a place of having yknow, clockwork orange karma ripping everything away from him

he leads the gang specifically alex through the dungeon before taking alex and separating him from the group, so you just go through that entire dungeon regrettably to get him back (though it can be said you need the golden bough at the end anyway soo) and find him like violently torturing alex with music from his past (singing machine aberration?) in an efforts to get him to kill himself which is VERY much working. rambles to the party about how they should leave alex to be "saved", if they truly care about him they'd leave him for dead. unfortunately no one in the gang does care for him so they save him.

golden bough is in the singing machine aberration, which is opened because alex commits suicide and feeds himself to it mid-battle as you're taking your time trying to deal with father alexander and his gangs (phase 1) and their music-posessed buffs (phase 2).

alex is revived and pulled out of the wreckage with something uncharacteristic (permanent scar on his neck)