This is one of the important quests in Fontain v4.0 that will unlock an area called the Institute of Natural Philosophy. You need to have access to this Insitute to complete the other 2 important quests too.
Rewards: Primogem x40, Hero’s Wit x3, Mora x33500 & Mystic Enhancement Ore x5
Achievement Unlocked: Twenty Thousand Leagues Under the Sea
➥ Talk to Virgil just near the Statue of the Seven in the Court of Fontaine. Spoilers: Don’t believe any sweet words he said, he can’t be trusted.
➥ The first task you need to do underwater is to search and collect clues. The first one is in between a barrel and a box. Keep following the trails and you will find more clues on top of more boxes. You will eventually enter the Liliacruces Forum’s former site (underwater ruin).
➥ When you’re at the ruin, absorb the Hunter’s Ray’s ability and use its ‘Water Blades’ skill to cut the weak link of the Seagrass above. Inside the triangle chest is an Ancient Key that you need for later.
➥ After that, use the ‘Water Blades’ skill again to cut the huge Fontemer Seagrass and destroy them to go forward.
➥ When you face a huge boulder blocking the way, absorb the Armored Crab’s ability and use its shockwave to shatter the stones so you can go forward. You can use the Ancient Key to the door inside that area. After that, keep following the quest navigation.
➥ Further inside the facility, go to the shining spot in front of the locked gate to continue the quest. You need to leave the water and talk to Virgil to talk about how to unlock the door.
➥ Now, to unlock the door, you need to take the Ousia Block on top of the ladder and aim it at the Pneumousia Relay with the Pneuma state (the left one) so that both mechanisms will be in a balanced state and you will unseal the switch to unlock the door in the water.
➥ After that keep following the quest navigation further into the ruin until you need to defeat the clockwork meka.
➥ Proceed deeper into the ruin and interact with the mechanism in the image above to increase the water level so you can go to the upper floor. On the upper floor, there will be a locked gate and you can unlock it by defeating the Ruin Guard in front of it.
➥ Inside the ‘treasure vault,’ you need to interact with 4 items: Kamera, Ruin Grader, cracked glass wall, and an Enhanced Pneumousia Amplifier. All of them have a shining spot in front of them so you won’t miss them.
➥ After Virgil not-so-surprisingly betrays you and locked you in, you need to fight the Special Ruin Grader. For the plot, this Ruin Grader can’t be defeated and you need to fight and wait until Paimon mentioned to break the cracked glass wall.
➥ Lastly, just follow the current until you reach Thalatta Submarine Canyon (Don’t teleport because this part is essential to continue the quest). At the end of the road, you will complete this quest, and a Luxurious Chest will appear near the teleport waypoint.
Rewards: Primogem x30, Hero’s Wit x2 & Mora x17000
Achievement Unlocked: A Fontainian Message
➥ Once you take the chest, teleport to the Statue of the Seven in Court of Fontaine and you will see two new people near the location where you first meet Virgil. Talk to them and tell them everything about what happened with Virgil to start the quest.
➥ After that, you need to go to the stronghold of Virgil with Sanie. Teleport to Elton Trench south waypoint and after arrival, swim deeper north into the deep sea following the navigation.
➥ When you reach the stronghold, a cutscene will automatically start with a group of untrustworthy people. You need to defeat all of them. After every mob is down, Virgil will appear so you can take revenge on him and defeat him too. Then, you will complete the quest.