Trilogy, in Night Ward, has a randomly ordered set of missions that, despite being out of order, do tell a general story once you've done all nine of them. I think it is not currently a story arc, but it feels like it should give merit rewards.
Would suggest either:
1. Make this a traditional story arc (leave the missions out of order, to keep a feeling of the current random order; roll some dice while you're turning it into an arc and just pick an order) with a merit reward at the end,
or...
2. Track the missions with a hidden badge, and give a merit reward when all of them are completed.
2b. Maybe even award a non-hidden badge at the end, such as something like "Well-Read".