My scum campaigns the first part is finished. The campaign got a “Pulp fiction”, “******”, “Lock stock and two smoking barrels” and “Oceans 11” tone, with heists and dark humor.
The players have been hunting the heretical drug Black and found some of it sources but suddenly then the whole thing goes quiet for a few years with no more leads to follow. The character have of course been sent into other missions during this time. The players have spun some sort of strange short stories about a few intervening missions during wild laughter at the gaming table.

The story is going to start again In media res at a schola.

Some kind of heretical cult have been replacing teachers at Schola Progeniums all over the sector in secrecy, and their Inquisitors who once was and still operates as a crime lord stumbled over that something fishy was about when one of his forgery businesses got on order of slightly altered versions of a prayer book. The traces lead to a schola. Following that trace futher the Inqvisition manage to observe a cult taking out a newly assigned teachers going to the schola (old war heroes, accomplishment adepts etc) and replacing them with false teachers. The inquisition silently intervened one of this operations and made a switch of their of sending the PC in as the false false-teachers.

The players will chose on their own what sort of teacher they pose as, but I suspect the Dusk born Moriat assasin with a bit sketchy view of the holy faith will be some kind of PA teacher.

They will start in media res at the schoola.

My thought is they should:
...Find some obscure trace of the drug Black again, perhaps a mention of a certain tech priest mentioned earlier.
...That the children will become suspicious and turn on the odd teachers/PC in a “Lord of the flies” way.
..That there of course will be some real cult at work.
...And perhaps they will have a run in with their antagonist stick-up-every-orifice Inquisitor Tormalkan.
(...And that there will be some Harry Potter references during the adventure.)

Pleas help me brainstorm, and come up some interesting twist and turns and scenes.

Actually, it's pretty similar to the idea I once had. But I'd go full on Harry Potter. Make them the kids, children of Imperial adepts (governor, Administratum prefect, head of a trade guild, minor Chartist captain etc) who perished in a Chaos invasion. They had to skulk in the ruins for a week or so, until an Imperial relief force arrived and recognised them for who they were. They're being sent by a ship to the nearest Schola. Run this as the HP Hogwarts Express chapter. Introduce a nice girl, pretty much a picture of Hermione - intelligent, a bit arrogant, but still likable. Make sure that they grow to like her, and that they get the HP reference. Then start hinting that she might have some unnatural talents - she is a psyker. So far everything is fine, they start forgetting the horror of the past few weeks. Then they arrive at the Schola, the head Sister greets them, warm and friendly, further making them feel safe. Then suddenly, one of the older students or Drill Abbot grabs the Hermione girl, stares her deep in the eye and recognizes that she's a witch. He tries to lynch her or burn at the pyre, but is only stopped by the Sister. Still, the girl is dragged away in chains. Cue the deconstruction of Harry Potter as it would occur in the grimdark world of 40k, maybe mixed with "Evil" ("Ondskan", a Swedish film about a private boarding school with a very weird code of conduct) - students denouncing their teachers as heretics just to pass an exam, brainwashing the kids into fanaticism, students enforcing their own brutal justice on younger kids, and of course a great evil of your own devising hidden at the heart of it, that nobody notices because they're to busy with their own interests.

It might be a bit different than your normal campaign and might be a bit too dark or shocking for sensitive gamers, but I'd say well worth it.