Marvel’s Wolverine: All In the Shadows Collectibles in Mission 16

Mission 16 of Marvel’s Wolverine, In the Shadows, runs Logan through a neon arcade, a stretch of rainy Tokyo rooftops, a construction yard, and The Hand’s hideout. It holds nine collectibles in total, and none of them are locked behind a one-time story beat.

Quick answer: In the Shadows contains 7 Material Crates and 2 Whisky Bottles, with no Nightmare Doors or Nightmare Trials. Collect them in objective order using the table below.

In the Shadows collectible list (Mission 16, Japan)

The list is ordered chronologically against the mission’s own objectives, so you can work down it from the top without backtracking. The pause-menu tracker shows how many items are still outstanding in the chapter at any point.

#	Type	Objective	Where
1	Material Crate	Investigate the arcade	Down the stairs past the main doors
2	Material Crate	Destroy more detectors	Left of the third detector, next roof
3	Whisky Bottle	Destroy more detectors	Balcony below the swing pole
4	Material Crate	Destroy more detectors	Upper roof corner, past the ramp
5	Material Crate	Destroy more detectors	End of the zipline, fourth detector
6	Material Crate	Eliminate The Hand	Construction yard, left of the digger
7	Whisky Bottle	Speak to The Chosen	Red-lit club room, back-left table
8	Material Crate	Catch up to Walter	Cave corridor alcove, on the left
9	Material Crate	Return to Shiro’s apartment	Drop off the zipline halfway

The two bottles are named Best There Is (#3) and Berserker Brew (#7). Material Crates feed suit crafting, which is how Logan’s maximum health goes up, so nothing here is purely cosmetic.

Arcade section: first crate and the That’s Cheating trophy

Enter the arcade and ignore the main doors ahead of you. Turn around instead and take the stairwell down into the lower storage area, where the first crate sits on the checkered floor beside the metal shelving.

Logan approaching a lit display inside the arcade building in Marvel's Wolverine — The illuminated arcade display Logan passes on the way through the building. Image: Insomniac Games

Head back up to the main arcade floor. During or after the fight, slash open every claw machine stuffed with plushies to unlock the That’s Cheating trophy. Missing one machine leaves the trophy locked, so sweep the whole room before leaving.

Logan tearing into a plush-toy claw machine on the arcade floor — Destroying a plush-filled claw cabinet, one of several needed for the That’s Cheating trophy. Image: Insomniac Games

Rooftop detector chase: three crates and Best There Is

Four of the nine pickups sit in the detector-destroying stretch across the rain-soaked rooftops. Use the third detector as your anchor point, because three of the four are reached from there.

Work your way up to the rooftops from street level, smashing the glowing power box and climbing the pole. At the third detector’s roof, face the detector, turn left, and jump to the adjacent roof for the crate sitting near the ventilation ducts.

Return to that same roof and look down below the swing pole. A blue scent trail marks the drop to a small balcony with an outdoor seating setup, where Best There Is rests on a round table beside a radio.

Logan crossing a wet Tokyo rooftop toward a red-lit objective marker — Traversing the rooftops during the detector objective, where the first whisky bottle is tucked below the swing pole. Image: Insomniac Games

Climb the tiled wall directly above the bottle, run up the wooden ramp, and swing across to the next roof. The crate is in the right-hand corner next to the large exhaust fans.

From the same roof, scale the big pipe and ride the zipline across. You land on an elevated platform beside the fourth detector, with the crate waiting there.

Enhanced Senses highlights the blue scent trail when a bottle is close, which is the fastest way to confirm you are on the right roof rather than the one below it.

Construction site and The Hand hideout

Once the noodle truck reaches the construction site, the mission shifts into an enclosed yard full of heavy machinery. Go left around the corner beside the digger and check behind the stacked pallets and bags for the crate before the fighting starts.

Logan running through a rainy construction yard past pipes and machinery — The construction site where The Hand defends the hideout, with the crate hidden in the left-hand corner. Image: Insomniac Games

Inside the hideout, the red-lit corridors open into a lounge area where you meet Jean. Berserker Brew sits on a small table at the back-left of that room, next to the armchairs. Grab it before advancing the conversation, since the scene moves you onward once you speak.

After the concealed revolving brick door opens, you follow a narrow wooden hallway and a concrete tunnel into a rock cavern while talking with Jean. Turn left into the alcove along the wall for the crate rather than running straight through.

Logan and Jean walking through a corridor with dialogue subtitles on screen — The conversation with Jean as Logan heads through the passage toward the cavern crate. Image: Insomniac Games

Final crate on the return to Shiro’s apartment

The last pickup comes after the Fist fight, during the trip back to Shiro’s apartment. Take the zipline across the street and drop off it roughly halfway, landing on the roof to your left where the crate sits behind the ventilation units and air conditioning gear. Riding the zipline to the end overshoots it.

How to confirm Mission 16 is fully cleared

Open the collectible tracker in the pause menu and check the In the Shadows entry. The finished state is:

Material Crates: 7 of 7
Whisky Bottles: 2 of 2
Nightmare Doors: 0 (none exist in this mission)
Nightmare Trials: none

Each crate awards +50 Materials on pickup, and the counter in the tracker updates immediately, so watch the number change rather than assuming an interaction registered. Story objects can look similar to collectibles, and the three collectible types count toward separate completion goals.

Nothing in Mission 16 is permanently missable. Once Mission Replay unlocks through the Nightmare Cabin, use the bed to return to In the Shadows; anything you already picked up stays collected, so you only need to grab what the tracker still lists as missing.

In the Shadows also unlocks the Marvel Tokon: Fighting Souls suit, and the crates you pull from it go straight into suit crafting. If you are chasing the full health upgrade or the crate-related trophies, clearing this chapter’s seven crates takes a chunk out of that total in one pass.