1st step: Get the orange ID card from Ballast E. There's a hard to notice vent; it has the card.
2nd step: Head to Ballast D, destroy the wall and head in. It's not considered part of the sub, so wear a suit and patch the hole after you're done. There's a safe at the end you can open with the orange card. Get the orange ID card.
3rd step: Head to Engine Bay 2. Right next to the left wall right above the engine is your next ID card.
4th step: Head to the cargo bay. In the bottom left corner of it, there's a safe with your next card, an endocrine booster, and a medal.
5th step: Head outside next to the two chainguns on the top of the sub. Right next to the left chaingun to the left is the next cabinet. It contains a nuclear scooter along with 3 medals.
6th step: Take the card and head back to Ballast E. In the top right there's a safe containing your reward.