To complete the Skullduggery quest in Metaphor: ReFantazio, follow these detailed steps:

### Step 1: Start the Skullduggery Quest

1. Progress in the Main Story: Ensure you have progressed far enough in the main story to unlock fast travel using the Gauntlet Runner.
2. Locate the Nervous Guard: Head to Grand Trad and find the Nervous Guard standing outside the entrance to the Grand Cathedral Mausoleum.
3. Initiate the Quest: Speak to the Nervous Guard to initiate the Skullduggery quest. This quest can only be started after 06/29 in the game’s timeline.

### Step 2: Gather Mortaskulls

1. Enter the Grand Cathedral Mausoleum: Fast-travel to the Grand Cathedral Mausoleum and enter it.
2. Locate Coffins: Walk close to the wooden coffins lining the walls of the Catacombs. This will make Skeleton Soldiers spawn from the coffins.
3. Defeat Skeleton Soldiers: Use Light and Strike damage to defeat the Skeleton Soldiers. Archetypes like Healer and Brawler are particularly effective against these enemies.
4. Collect Mortaskulls: Once a Skeleton Soldier is defeated, it will drop a Mortaskull. Repeat this process until you have collected eight Mortaskulls.

### Step 3: Avoid the Bug

1. Complete Both Quests Simultaneously: To avoid the bug that prevents Skeleton Soldiers from spawning, ensure you have accepted and are actively working on both the Skullduggery and Haunted Heirloom quests simultaneously. This will prevent the bug from occurring.
2. Reload Save if Necessary: If you encounter the bug and Skeleton Soldiers stop spawning, reload your save from an earlier point in the game. If reloading is not possible, wait until the in-game deadline of July 30 passes, and the quest will fail and be removed from your quest log.

### Step 4: Complete the Quest

1. Notify Gallica: Once you have collected all eight Mortaskulls, Gallica (your follower) will comment that you have what you need to complete the quest.
2. Return to the Nervous Guard: Go back to the entrance of the Grand Cathedral Mausoleum and speak to the Nervous Guard to turn in the quest.
3. Receive Rewards: After completing the quest, you will receive a Brigandine armor piece and 3,000 Reeve as rewards.

By following these steps, you should be able to complete the Skullduggery quest in Metaphor: ReFantazio without encountering the bug that prevents Skeleton Soldiers from spawning.