After activating all the terminals in Divine Beast Vah Ruta, Waterblight Ganon emerges from the Main Control Unit.
Waterblight Ganon's eye is its weak point, so you can try shooting the eye to reduce Ganon's HP. A direct hit with a shock arrow can knock Ganon down.
Waterblight Ganon is weak to ancient weapons and Guardian weapons, so equip those if you have them.
Waterblight Ganon can jab with the spear or swipe sideways with it. If you are quick, you can jump out of the way of these attacks, allowing you to do a Flurry Rush.
You can also destroy Waterblight Ganon's spear if you use Cryonis to create an ice pillar in the path of the spear's attack. The spear will shatter if it hits the ice pillar, giving you a chance to run up to Ganon and hit it with your melee weapon, or to just shoot its eye from a distance. However, Waterblight Ganon can create a new spear shortly after the previous one is destroyed, so be ready to run away afterward.
Waterblight Ganon might also throw his spear at you, so be prepared to sidestep it if you see Ganon reach back to throw it.
Waterblight Ganon can also attack with an energy field if you are standing too close. It will point its spear down and charge up the attack, so if you see this happening, run away so you won't get hit.
Waterblight Ganon can also teleport around the battlefield. Make sure that you are not close to the spot where Ganon will reappear.
After you reduce Waterblight Ganon's HP to 50%, some platforms will rise from the water. Climb onto one of these platforms, but not the one that Ganon is floating over.
Switch to the Cryonis rune so you can destroy the ice blocks that Waterblight Ganon can shoot at you.
Sometimes you will need to swim to another platform. You might not want to dash in the water, because Link can't climb onto the platforms until after he is finished dashing.
Whenever you can, shoot Waterblight Ganon's eye with an arrow. If you hit the eye, Waterblight Ganon will fall down and you can attack it repeatedly before it gets up.
After you defeat Waterblight Ganon, you will get a Heart Container. Then, examine the Main Control Unit to activate it. The game will warn you that you won't be able to re-enter the interior of the Divine Beast after this, so if you want to explore more, say No.
You can use the Hyrule Compendium to search for treasure chests in the Divine Beast if you think that you missed any. You can take a picture of an opened treasure chest if you haven't added treasure chests to your compendium yet.
After you activate the Main Control Unit, you receive Mipha's Grace, which will revive you and give you bonus hearts if you lose all your hearts. It takes 30 minutes to recharge afterward. You can disable (and re-enable) Mipha's Grace in your inventory.
There is a cut scene where the king asks you to take the treasure in the chest next to the throne. The chest contains the Lightscale Trident, a weapon that Mipha wielded. This weapon can break, but you can talk to a blacksmith Zora in Zora's Domain and ask him to repair it. You will need to bring him a Zora's Spear, some Flint, and a Diamond to do so.
After this, you can talk to the king to tell him of Mipha's fate.