In this case, mission are sequences that are required in order to progress the plot. Dungeons are pretty important, but without the missions in between, a Zelda game would be incomplete. Whether it's a stealth mission, escort mission, an item mission, or anything in between, these, in my opinion, are the greatest in the whole Zelda series. ( In no particular order)
Hidden Village- Twilight Princess
The Hidden Village once served as the secret home to the Sheikah tribe; however, due to the "prolonged wars," the tribe dwindled and the town fell into decline, becoming infested with Bulblins and leaving only one resident, Impaz, who is seemingly the only person that can restore the memories of your dear friend, Llia. When Link first visits the town, it is infested by 20 Bulblins, all of which he must slay in order to rescue Ilia's helper. Impaz, comes out of her home after Link slays every single one of the beasts. Thanking the young hero for his help in defeating the Bulblins, she hands Link the Horse Call which is an item Llia gave to Impaz before escaping the Hidden Village, which helps her gain back her memories. This is a great mission in my opinion because of the sheer fun. Taking on a sort of cowboy theme, Link uses his bow to shoot down the Bulblins one by one while rodeo music plays in the background. You just feel like a total boss. If you have your Hawk's Eye, it's even more fun. Also, once you rid the land of enemies, kittens come out to play with you... Which is always a plus.
Eldin Volcano Dragon Quest- Skyward Sword
Upon entering the Eldin Volcano for at least the 3rd time, you are greeted by an irrupting volcano that makes you crash land. When you come to, you're imprisoned by Bokoblins with absolutely no items. Since luck is your side, some Mogmas decide to thank you for saving them at the Fire Sanctuary and give you the Mogma Mitts, letting you escape your confinement. Now all you have to do is get all your items back... Too bad it won't be that easy. The whole Volcano Summit is littered with Bokoblins that want to end your life. Even though stealth is not my favorite thing, I absolutely love this mission because of how awesome it feels once you get your items back one by one, and you figure out that all of them are completely necessary. With the slingshot, you can stun patrolling Bokoblins, making it so much easier to sneak around. With the Clawshots, you can zip around on floating plants, making for some fast and quieter transportation. With bombs, you can explode everything in your way... And that is awesome. Even the Gust Bellows, probably the most useless item in the game, is extremely useful in this part. And look at it this way: In this stealth mission, if the patrolling Bokoblins catch you, you don't have to starting from the freaking beginning. ( I'm looking at you, Wind Waker...)
Infiltrating Hyrule Castle- Link to the Past
"Help me...
"Please help me...
I am a prisoner in the dungeon of the castle. My name is Zelda..."
With these fateful words, your quest to save Hyrule from utter destruction begins.
Your uncle awakens you to say he'll be back by morning, with an order not to leave the house. Bearing a sword and shield, he leaves. But with your curiosity getting the better of you; you go against your uncle's orders and attempt to rescue Zelda. Once you leave the house, it's dark and pouring rain. As ominous music plays, you hear Zelda's pleas faintly. You then find yourself at Hyrule Castle, with armed soldiers at every door. You try talking to them, but they assure you that your just a kid and that you should go back to bed. This combination elements set the mood perfectly- bad things were happening, and no one believes a kid could do anything of real significance. Then how do you get into the castle? It's certainly heavily guarded... If you wait long enough, Zelda will contact you again to tell you of a secret passage somewhere near the castle. To your right there is a large, white boulder that you cannot lift. Go north. At the end of the path is a bush with a stone border around it. Lift it to reveal a hole.
Be brave and step into the hole. You land in a shallow pool of water.
When you head, you find your uncle, mortally injured. He gives you his sword and shield and tells you in his dying breath how to wield the blade that now belongs to you. As you go throughout the castle, you find soldiers patrolling the halls. They attack you with no hesitation, so surely they're being controlled by some powerful entity. You cut them down, with no remorse. As you get deeper into the castle, the guards get more powerful and bigger in number, but that doesn't stop you. You get to basement of the castle and finally find the cell containing Princess Zelda! But guarding her cell is a soldier wielding a ball and chain. Your strategy is to run in close and hit it, then run away fast before it spins its ball and chain. You know it's about to spin it when it stops moving for a second, so don't get close if it stops for very long. If you lose hearts while fighting it, get some from the pots in the cell. Once he's defeated, you receive the key to Zelda's cell. Once you unlock her, Zelda tells you about the wizard named Agahnim, who has taken the castle by force. Other missing girls have fallen prey to the wizard's dark magic. Agahnim plans to break the legendary seal of the seven wise men, which will spread untold evil across the land. With this knowledge, you escape with Zelda and officially start your adventure. If you can't tell why I love this mission, than I don't know what to say to you. The whole set up is practically PERFECT. Yes, the word needed all caps. An amazing start to an amazing game.
What's your favorite mission in Zelda? Comment below and thanks for reading!