You can find the Scanner in the submerged control room of Sea Mauville. This item is hidden, so you will need to stand at the exact spot where it’s located to obtain it.
You will also need HM03 Surf and HM07 Dive (along with the Mind Badge) to access Sea Mauville and its underwater basement area.
The Scanner is a Key Item used to trade for the Clear Bell or the Tidal Bell, depending on your game version.
Scanner Location (Step-by-Step)
Its fully submerged control room is underwater, requiring HM07 Dive, and you can access that only from inside the ship.
Step 1: From the deck of Sea Mauville, head north.
Step 2: Once you’re on the deck, go east and turn towards the entrance (south) to go inside.
But before heading inside, you can speak to the Scientist NPC nearby. He’s tasked to look for the Scanner by Captain Stern, and you’ll find him just north of the entrance.
Step 3: Once inside, go southwest and eventually turn to head directly south until you find the water.
Step 4: Use Surf to move forward and reach the darker patch of water, then use Dive to enter the underwater area of Sea Mauville.
Step 5: Once underwater, head directly south.
Step 6: Turn east at the corner, then turn south towards the stairs leading to the control room.
Step 7: In the control room, take the staircase on the right and head to the spot directly in front of the bottom of the stairs (circled below).
This is the exact location where the Scanner is located.
Just remember that the Scanner is a hidden item. Standing at the exact spot of its location will trigger the dialogue to pick it up.
What is the Scanner Used For?
The Scanner is primarily used to obtain two other key items (Clear Bell or Tidal Bell).
Once you acquire the Scanner, you can speak to Captain Stern in the Slateport City Harbor to exchange it for the Clear Bell (Omega Ruby) or the Tidal Bell (Alpha Sapphire).
You can then return to Sea Mauville with the Clear Bell to encounter Ho-Oh, or return with the Tidal Bell to encounter Lugia.