The ending of Chapter 2 of Resident Evil 4 Remake has left Leon in a... strange situation. It looks as though every chapter is going to end with something unpleasant happening, only for it to be resolved afterwards... or perhaps not. Once you regain control of Leon, interact with the painting on the wall and activate the lever. You cannot climb up there yet, but remember this location.
Open the door and head outside. Go around the house to free a dog. Then head north and follow the path to return to the Village. First, go to the northern part of the Village and use the Small Key on the locked drawer to obtain the Vintage Compass. Remember to collect the Velvet Blue and the Ruby as well if you did not pick them up during the previous chapter.
Once the tower collapses, if it did not already fall while you were exploring, several infected dogs will appear. Be careful, as they move quickly and can be difficult to hit. Fortunately, they cannot withstand much damage. Before continuing, you can return to the Farm to obtain another Pearl Pendant and another Ruby. You cannot travel northeast to the area where you found Luis, at least not yet.
To continue, you need to get around the tower debris in the Village Square by heading northeast and passing through the house. If you want to avoid the enemies, there is a well in the southern part of the Village. Climb down the ladder, go through the tunnel and emerge beside the gate to avoid the dangerous dogs. After passing through it, you will enter the Town Hall. There is a Viper inside a crate, so kill it and then pick it up.
There are several items in the area, including one hanging from a lantern and marked on the map: a Velvet Blue. Afterwards, continue until you reach the Merchant. Beside him, you will find the note for the Viper Hunter request. You cannot complete it yet, so continue until a cutscene plays when you try to enter the church at the top of the graveyard.
If you open the map, you will see two icons showing the locations of treasures. Head to the one southeast of the church to find the Elegant Headdress. You cannot reach the other treasure yet. Beside the headdress, you will find the Grave Robber request, which you can complete immediately.
To continue, go to the southwestern wall of the church, where you will find a door just before the alleyway. Enter, collect the items and open the hatch leading to the basement. Drop down and follow the uphill path to unlock the gate, then head south across the bridges. Watch out for the enemies and collect the second Viper inside the shed you pass along the way.
You will notice that one of the treasures is level with the bridge, but outside it. Stand near the icon and you will spot another lantern that you can shoot down. You cannot collect the item yet, but it will be within reach once you move forwards. Proceed through the tunnel while watching out for explosives and cross to the other side. As soon as you reach the Quarry, you will see a notice indicating that there are Blue Medallions nearby. This is a large area, so keep an eye out for these medallions as you progress.
Be careful of the dogs in the Quarry. There is a treasure hanging from a lantern in the middle of the area. Shoot it down to collect another Ruby. You will also see the first medallion on a tower. As you continue, you will pass another locked chest that you cannot open yet. Keep going and descend the stairs. On your left, you will find a chest containing Hexagon Piece A. Alongside the Merchant, you will also see an elevator leading to the first Shooting Range. Try to achieve at least the target scores so you can obtain some useful charms.
Before continuing, climb down the ladders and head to the southeastern end of the dock to destroy Clockwork Castellan #03.
Then leave through the northern exit and use the binoculars at the observation point to see... something. Something you know the identity of, right? Afterwards, look to the right to spot a boathouse.
Continue forwards and head west when possible, in the opposite direction from your objective. You will reach the Fish Farm. Start by eliminating every enemy and then check the map. You should see a treasure and three Blue Medallions belonging to the Quarry and Fish Farm area.
The treasure is an Antique Pipe hanging from a lantern. Shoot it down and collect it. Then, in the northern section, near the northernmost Blue Medallion in this area, you will find a chest containing Hexagon Piece B.
Finally, to wrap things up, there is at least one Viper in the water. They move around, so you will need to search until you find one, shoot it and pick it up. You should now have three Vipers (it does not matter if you sold them after accepting the request), allowing you to complete Viper Hunter.
Now head to the westernmost building, where you will find a can of Boat Fuel. Beside the building, slightly to the south and before the water, you will see a small shed. There is a Small Key on a table inside, so make sure you collect it.
To head back, use the ladder to the south, which will take you to the area where the crossbow-wielding enemies were positioned. Be careful, as more Ganados will appear and climb up the same way you did. From there, you can return to the eastern side, climb another ladder and make your way back to the Lake. Climb down to destroy the final medallion in this area and collect several items. You will also see a stone pedestal where the Hexagon Pieces must be placed, although you are obviously still missing one.
Return to the Merchant to hand in both requests involving the Vipers and Blue Medallions. If you descend the stairs beside him, the map will mark a treasure inside a locked drawer. You have a Small Key, so use it to obtain a Brass Pocket Watch. Return to the lakeshore and start the boat (damn, I am a poet). Once you regain control of Leon, remain calm and throw harpoons at the creature until it submerges and the boat comes to a stop.
When this happens, wait for the monster to resurface and follow it. Eventually, it will charge directly at you. You must throw a harpoon into its open mouth and repeat the process until it is defeated. If it leaps towards you without first stopping the boat, steer to one side to dodge it. Bear in mind that every harpoon deals damage, so you can shorten the fight considerably by attacking whenever possible, but make sure you remain ready to dodge.
Once you defeat the beast, you will proceed to Chapter 4.
