In order to collect the Submarine Parts, you need to purchase Sonar Collections Docks for $250,000 (can be purchased by anyone). As Michael, you then go to the ? at the docks and meet with Abigail, which will trigger you being able to find the pieces.
A Dinghy becomes available at the docks and is fitted with sonar. When you get in, a green circle will appear on the map, so go there and then the sonar will start pinging. Dive underwater (you get scuba gear, so no need to worry about your air supply) and use the pings to help locate the parts. Note that the parts flash, so be on the lookout for that when looking for them.
Note that there is likely to be some sharks at some of the wreckage sites. They will appear as red blips on your radar if they are there. If you do spot them, you can either try to kill them with a knife, or you can hop back into your Dinghy and attempt to run them over with it. There is usually only one shark at the spots where they can appear.
Submarine Piece #1
It is located at the first green circle. Dive down and follow the ping until you spot it near the piece of a wrecked plane. A health kit is close by.
Submarine Piece #2
It is located at the first green circle. After collecting #1, head towards the next ping and you'll find it inside of the main body of a wrecked plane.
Submarine Piece #3
It is located at the first green circle. After collecting #2, dive over the edge of the cliff and all the way to the floor, where you'll find it sitting next to a wrecked plane's engine.
Submarine Piece #4
It is located at the second green circle. Beware of sharks in the area, as you dive straight down in the middle of the circle to find the piece next to some engine.
Submarine Piece #5
It is located at the second green circle. From #4, go to the next blip and you'll see a huge plane. Go inside the plane to find the piece, which is next to some body armor.
Submarine Piece #6
It is located at the second green circle. From #5, go out the other side of the huge plane and you should see it directly below you.
Submarine Piece #7
It is located at the second green circle. From #6, head towards the next ping and locate the landing gear of a plane in the water. The piece is in between the wheel and a piece of debris.
Submarine Piece #8
It is located at the second green circle. After collecting #7, head to the next blip and find the piece of plane you can go inside. Do that and find the ladder at the back of this piece. The submarine piece is on the ground next to the ladder.
Submarine Piece #9
It is located at the third green circle. There are sharks in the area, so be careful. Dive underwater and you should see a huge sunken ship. This piece is under the stairs on the deck of the ship.
Submarine Piece #10
It is located at the third green circle. After collecting #9, go to the end of the ship and you'll see it sitting on some debris just past the ship.
Submarine Piece #11
It is located at the fourth green circle. Once you get there, dive down and you should see it next to some metal framing debris.
Submarine Piece #12
It is located at the fifth green circle. Get there and dive underwater, to find the piece underneath the docks.
Submarine Piece #13
It is located at the sixth green circle. This piece is next to a destroyed tower of some kind.
Submarine Piece #14
It is located at the seventh green circle. This piece is located to some metal debris on the ground.
Submarine Piece #15
It is located at the eighth green circle. It's next to a pillar of sorts, which has three rods.
Submarine Piece #16
It is located at the ninth green circle, which is very close to the eighth one, so it overlaps some. It's next to some metal debris on the floor.
Submarine Piece #17
This one is similar to the last one, as it's a completely different green circle, but might overlap with the previous one some. It's next to two metal pipes of some kind sticking out of the ground.
Submarine Piece #18
It is located at the eleventh green circle. It's on top of some debris, which appears to be wood.
Submarine Piece #19
It is located at the twelfth green circle. There will be sharks in the area, so be careful. There is a huge wrecked plane under the water and you'll find this piece underneath the right rear wing.
Submarine Piece #20
It is located at the twelfth green circle. After collecting #19, head to the other side of the plane and look under the debris near the back for this piece.
Submarine Piece #21
It is located at the twelfth green circle. After getting #20, head to the front of the plane and you'll find an opening, with the sub piece right there.
Submarine Piece #22
It is located at the thirteenth green circle. Dive underwater there and you'll see a large pipeline. The piece is sitting at the opening of this pipeline.
Submarine Piece #23
It is located at the fourteenth green circle. There is a rock circle, with the piece being underneath it.
Submarine Piece #24
It is located at the fifteenth green circle. You can find it right on top of some debris.
Submarine Piece #25
It is located at the sixteenth green circle. There is a huge sunken ship and the piece is right on the deck of this ship.
Submarine Piece #26
It is located at the sixteenth green circle. After collecting #25, go towards the edge of the ship and you should see an opening with some cargo containers. The piece is in that opening.
Submarine Piece #27
It is located in the same area as the previous two. There's another large chunk of the sunken ship past #26. Go inside and you'll find it on the floor.
Submarine Piece #28
It is located in the same area as the previous pieces. Stay along the ocean floor and swim to the next marker. The piece is underneath the actual ship itself.
Submarine Piece #29
It is located at the very last green circle, which is northeast of Mount Gordo. It is next to some rocks on the ocean floor.
Submarine Piece #30
It is located at the very last green circle, which is northeast of Mount Gordo. It is next to some rocks on the ocean floor, but not at the same spot as the previous piece.
