After heading up the first set of stairs after touching the podium go around the ship to your left

In the same room atop a bunch of boxes to the right of the button podium

Inside the room of cells you start in, on the left side behind a synergy attack wall

At the first 3 way intersection go left and it is in a octagonal room out in the open

After you quell the riot with Spider-Man take a right at the 3 way intersection and it is behind a breakable wall

Right before the sandman fight go left of the button podium to find it out in the open

In the cafeteria after the two laser grid pathways, look at the bank of cells on the left and it is in the last one

In the top right most corner of the first 6 grid puzzle

In the room following the 6 grid puzzle look to the cells on the left and go to the 2nd to last one

Top right most corner in the 12 room puzzle grid

In the bottom right corner of the 12 grid puzzle (off screen) is another out in the open

Directly after the 12 room grid puzzle there is a synergy door to the right (adjust camera accordingly)

Defeat the Spider-Gwen/Miles Morales/Kamala Khan

In the second part of the spotlight stealth section it is in the north of a "H" shaped intersection behind a synergy wall

After you first meet Jessica and get to the red bridge head across the way, the box is sitting out in the open near a building

After you solve the first puzzle for the door it will be behind a banner directly in front of your path

Before you enter the room to help Daredevil you will see a pile of boxes in front of you, break them and the banner behind them

After you beat Elektra and are about to go about the stairs break the boxes to the right of them

After the stairs break the second banner on your right and angle your camera to the right

As you exit this hallway it will be immediately to the right of you

As you exit the room you will see a synergy block right in front of you

As you are about to head up the elevator to Kingpin it is in the top right corner of your room behind a synergy wall

Before you head into the doors to Kingpin go left to find one out in the open

The first room you run into with all the wreckage, it is one of the cells to the right behind a synergy wall

In that same room in the upper left you can jump on some rubble, go left and follow the path forward

Following the normal level path it will be a breakable wall in front of you, cant miss it

Located in the first honeycomb room, top right of the room cant miss it

Right behind Thor at the checkpoint, should be out in the open

Found inside the second honeycomb room in the middle of the puzzle on the right side

Found in the same second honeycomb room at the top of the room out in the open

After you activate the console turn around and head into an alcove with a bunch of boxes, it is out in the open

Defeat Ultron (seems to count for multiple boxes)

Right as you head up the elevator to deal with Ultimo look to the right as the camera becomes free

Defeat the Infinity Stone Sentinal

Defeat or Lose to the Brotherhood of Mutants

At this Checkpoint go left into a little off area then go left again and it will be in the open

In the room following the checkpoint look to the wall to the left to find a synergy wall

The room after the previous rare box room break the book cases on the right had side and it will open a hidden room

After heading down some stairs there will be a synergy box out in the open

After you survive the danger room take a left at the first intersection, it is behind a synergy wall

Continue down the path from the previous rare box, it will be on the right before you head up the set of stairs

Defeat Corvus Glaive/Proxima Midnight

After the second large cliff drop go right and it is right around the corner

Right before you enter the portal in this area to unlock the barrier look to the left and you will see a synergy wall

About halfway through the first 2d walkway there will be a pitfall under a platform take it to fall into a portal and get to another platform with the rare box

Restore Doctor Strange's Sanity

At the second 2d walkway, drop down and walk to the left to destroy the red barrier, head forward to a rising platform and jump on it to reach a rare box

Walk past the portal out of the second 2d walkway and it will be out in the open

After you take a portal you will see 3 behind a barrier, take a orb and get hit to destroy the red artifact, take the portal to destroy the yellow barrier then head back to collect

Keep heading forward from the previous boxes and you will see one in a synergy block out in the open

Before you head into the portal into the next area look to the left of the path, you should see a slight glint

As you are about to get to the next checkpoint go right at the 3 way intersection on the zig zagging platforms and it will be behind a synergy wall

Has no Rare Boxe's

In the first open area where you fight enemies it can be found on the right side on cliff near two enemies

After you first meet Storm there will be a synergy wall on the right hand side of the room

At the first area where you have to break a power source, head left along the cliffside before you head through the arch, it will be on the other side of a climbable surface in front of you

As you exit the arch from the previous box and head down the path, it will be on the left behind some boxes before you head into the next room

It is the next room with the first set of turrets you will face, it can be found atop a cliffside on the right side of the area

In the open with snipers in front and on your left cliffside, head up to the cliffside and head to the drop off and it will be there out in the open

During the bridge portion with the panther laser it will be found in a synergy box about halfway on the left

Follow straight ahead from the checkpoint, once you reach an outside area it should be on your right side inside a small area with broken walls

As you head into the next group of enemies you should see some stairs on your left leading up to a synergy wall

Before you head into the next area with snipers you will notice a odd colored breakable wall on your right it is behind that

Upon entering a square room with snipers up on a elevated platform you will want to go around to the south eastern corner and you will find yourself in another room with 3 turrets

Once you hit the second open room full of enemies you will see a small platform on the left jump on that and head up

Upon following the path you will run across a abnormally large pool of green on the upper right of your screen, walk through it to find the box on the other side

Following the bottom path of the 2d walkway you will find it behind a pool of green

Found in the 2d walkway inside the palace, easily seen

Seen in the same pathway as the last box, easily noticable

Easily seen in a synergy block in front of you as you exit the 2d walkway

Can be found inside an alcove in the statue on the opposite side of the entrance, will have to rotate the camera to see

If you look to the left as you enter the room to this checkpoint you will notice a synergy wall to the left side

As you release the second set of Asgardian prisoners it will be found in the first cell on the left

Continue the path past the second set of Asgard Prisoners you will see a synergy box right in front of you