Let me first say this. You most likely mean third Chapter, because the third act kinda starts from the moment that Link decides to go to the final dungeon to defeat Ganon. The third act is the hero's resolve, where he finally overcomes his shortcomings. Acts and chapters are different. Each good story always has 3 acts, but can have an arbitrary number of chapters.
Okay, now let me get back to the point. This is my idea about the Zora part:
The ZolaInstead of making them river Zola, may be they are Zola from a far away land. They are something like the Vikings in Europe's past. They have come to Hyrule (up the river) to plunder and pillage everything. Because the Zora's look similar and are also aquatic creatures the Zola see the Zora as the biggest thread. The Zola have put up their stronghold downstream in River Valley near the entrance to Lake Hylia. Effectively blocking access to Lake Hylia for everyone.
StoryThis the story I thought up with the above idea for the Zola. Before going immediately to the Zora area, it is probably better for Link to go back to Castle Town for some story bits. This also shows the player that there is an opportunity to take up sidequests in Castle Town and interact with with the gang and other people.
First Link goes back to the Gerudo King. The King tells Link that he found out about the possible locations for 2 more cogs from the Castle Library. These cogs were taken into care by a Zora and a Goron family. Link should visit them for the cogs. If Link tries to go to Goron Mountain he finds his way blocked due to a landslide. Some Gorons are working on clearing the path.
Link can also not go to the inner part of Zora's Domain yet, because he cannot swim. Zora's Domain inner part where the Zora have retreated is only reachable through swimming as this gives better protection against enemies and especially land monsters. (I know the GDD says the flippers are granted to Link by the Zora royalty, but bare with me for now)
In Castle Town Link meets a Distressed Deku Merchant, who tells Link that Zola bandits robbed him of his merchandise. Seeing that Link has a sword he asks him for help. Link sets out to get the merchandise back from the Zola. Link finds the Zola raiding party that stole the merchandise and defeats them. As Link picks up the merchandise he is attacked by another party and a Huge Zola, who is apparently their leader. The Zola leader knocks Link out cold. As Link passes out the leader orders his men to leave Link alone, because they just caught a more valuable price (a reference to the kidnapped royal children) that they need to haul back quickly.
As Link wakes up he returns the merchandise to the Deku merchant in Castle Town. The merchant is so gratefull that he offers Link his stuff for a reduced price. Among the stuff is a pair of flippers the merchant wanted to sell to a rich guy for 10.000 ruppees, but he is willing to give it to Link for merely 100 ruppees. The flippers were created by a Goron who wanted to visit the Zora once, but once he finished the flippers it seems that they were to small to keep a Goron afloat.
Link buys the flippers and can now swim to Zora's Domain to meet the Zora King. Zora tell him about the tragedy that has befallen them and that they can no longer go to there sacred place in Lake Hylia to pray for a good ending. One of the Zola Raiding parties under the Zola leader succeeded in kidnapping the Zora royal children and bring them to the Zola stronghold near the entrance to Lake Hylia. They are ransoming them, but the Zora are proud and the King is scared that they will ransom more or even get killed anyway. In addition is the plundering of the Zola also a big problem for the traders traveling through River Valley.
Eventually Link is asked by the Zora King to use his thieving skills to sneak through the back into the Zola's stronghold and rescue the kidnapped children. If Link incidentally defeats their leader in the process it will be a benefit. Link goes to rescue the children, but gets caught by the Zola leader. This time Link defeats him and the Zola scatter. The Zora warriors then enter the stronghold to get the children back. After this it will be more quiet, but there will still be Zola raiding party around.
Link can then continue to Lake Hylia. Somewhere in Lake Hylia Link sees a large patch of Ice. On the shore is a hut of the smithy brother Sheldon. He tells Link the story about some ancient devices along Lake Hylia 's shore that can raise the Temple's entrance above water level. He knows of one such device, but has never been able to successfully raise the Temple entrance, so he thinks there are more such devices.
Link sets out to find the (3) devices. At the first device he meets Maple, who was told the same by the ancient hero. She uses her magic on the device to turn it on, but accidentally destroys it. Link asks Sheldon's help to fix it. Sheldon can fix it, but he requires materials which were difficult to get due to the Zola blockade. Link has to get materials from various areas in Hyrule.
After Link brings him the materials, Sheldon starts fixing the device. Link will look for the second device. After he turns on the second device and emerges from the hidden cave, Link is attacked by some Zola. They want revenge on Link for defeating their leader.
For the third device Link has to find a dive spot next to Lake Hylia's cliffs. Diving in this spot, makes Link emerge in a hidden underground cavern where the third device is. Once Link emerges from this cave, Sheldon turns on the first device and the entrance to Temple will burst out through the ice spot, leaving only a small spot of Ice for Link to climb on and Link to enter the dungeon. However Maple flies in before him.
Inside the dungeon Link will meet Maple again, where she has been knocked out cold by the mini-boss of the temple. She will be out cold and seeing stars until Link has left the temple with the cog.
I like the MG's of the Deity conflict. I'd assume the Zola's deity would be their Deity of War, Sacrifice and Competition.
If that be so, what'd we have the Zora's deity be as?
I also think that the temple idea could be a good addition, make it so there was more of a spark for the war, making the Zola feel that the Zora crossed the line too far.
I think you might be carefull with naming deities to abstract ideals and such. In every Zelda game there are three Goddesses as the highest deities in Hyrule. There are some lower deities, but they primarily guardians of a race or land. Such as Jabu Jabu, Deku Tree, Valloo and so on.
