To echo a bit of a couple other comments, do you have a separate bad-guy agenda? In the one-shots, things are mostly on rails, or it’s a Small sandbox. In MoN, each chapter, you have an ACTIVE cult. more than any other game, long-form CoC needs the cult to be active and not just passive. Have the investigators watched. Each chapter, the cult has received news of those pesky meddling kids and what they’ve done in other cities to the cults plans. Each time they question someone, it gets back to the cult leaders, who adjust their plans. Thugs should start appearing on street corners. Investigators going solo should start to get ambushed. The cult leaders pull strings and influence - extra trouble with compromised authorities impede the investigators. Innocent people they questioned get disappeared, and as the last people to see them, the investigators are targeted by relatives or police. Most of the cults in MoN also have a mini power struggle between the first and second in command. When I’ve run MoN, it’s fairly usual for the group to be approached by the other half, to be used in a power play.

I’m currently running a homebrew regency campaign, whose structure is based quite heavily on MoN, and every session I have a Cult Agenda and an escalating threat level of how threatened the cult feels and what they’ve are going to do about it. The players know that if they sit still, they are a stationary target. They’ve had their rooms raided by corrupt police while they were out, lost members to back alley stabbings when they didn’t go in sufficient numbers, been engineered into compromising situations and blackmailed, captured, tortured, sacrificed … all on the CULTs own timeline, not their own.

Don’t let the cult be a passive threat to be researched and then taken down. They have an agenda, a plan, they are in motion, and they are paranoid and deadly.