I have a beginning and a partial end, but no fully developed middle.

The characters that are playing this are a genasi fighter and a paladin dragonborne. The story takes place in a small partially developed medieval city called Norbury run by the duke of the town. It begins a day before the harvest festival, and the local tourney. The genasi works for the duke, while the paladin is independant. (Backstory is that he was kicked out of the church for saving a family of sinners who didn't want to convert) At the very beginning, the genasi is kneeling before the king who is all like, "Harvest Festival tourney match is coming up... you know what to do." Fighter, meanwhile, saves a child from a runaway wagon where a kid looks at him in awe, and directs him towards a board for an advertisement surrounded by a bunch of MISSSING posters. (that's important down the road.) This is where the two PC's first meet. Later, after the competition/exhibition fighting match, the fighter is approached by a woman all distraught in a bar, asking for someone to save her child.(It's the boy from before, and I promise I'm subtle) The duke is either scalding or poorly/sarcastically congratulating the fighter... until a guard burst through the doors exclaiming that goblins have just stolen the duke's son from the royal garden. Both PC's find each other while doing this quest again (Go on some goblin raid) BOOM! Boss Room!

They take out the goblin encounter, and slowly make their way to the boss room. Dim light is being shown through a small gap in the ceiling leading to the surface mainly blocked off by rubble. There are eight goblins on the ground bowing down to this giant 2 ft. white maggot on a tattered, stained purple silk pillow in the middle of the room around a circle of this weird gooey substance while chanting. On a stand, behind a pedestal in the very back, there is this monstrously sized goblin with tight leather overall straps made of leather and a sword strapped to him made of what looks like bones and a small hunched cloaked figure is on a stand speaking to the crowd in a language you do not understand. The two boys are on the ground right in front of the pedestal, collapsed, tied up, and unconscious. “We will now do the choosening!”
This causes an eruption of cheer.
“Through this sacrifice will our God be born and we will reclaim our lands once again!”
More cheering

    Turns to figures- “Now, you promised us first pick this time since this will be the last thing we need for our God to be reborn.”
The hooded figures hesitate, and then slowly nod in agreement. The boss slowly makes his way to the two boys that are being guarded by a goblin dressed like a girl. The boss is examining the noble boy with a keenful eye, and kicks the goblin square in the chest, sending it flying across the room. “How dare you come back here with this trash! Did you truly think this human is of good enough quality to give to our allies, or were you just wanting to die tonight?!”  *picks up the limp goblin* “At least through death, will your useless self actually amount to anything. Sacrifice you body. Let your flesh be the nutrients for our God so that you may be reborn again through him!” This dark figure starts to shuffle towards the goblin and produces what looks like this dark inky liquid and empties the contents into the goblin’s mouth, and they toss him at the foot of the pillar with the maggot on it, and nothing seems to happen at first, but then the goblin’s body begins to violently shake while it’s eyes turn pitch black. It mouth opens of to only make gargling noises, and you watch in horror as this creature turns into a mound of oozing flesh with teeth and eyes. It slowly inches away from where the body once stood, and joins the rest of the flesh circle.
“You take this one then”
*hands noble boy over, which the second figure takes shoves in the basket, and then scrambles up the rubble into the small hole of light.
“REJOICE! We have finally gathered enough raw material. And with the aid of our allies, we will  be in possession of the last ingredient… the blood of a celestial.”



The cloaked figure produces another vial, this containing an yellowish-orange fluid and proceeds to pour it onto the flesh. The flesh when coming into contact with the fluid instantly shoot out and incase the boy in a see-through pod of flesh, and a fleshy tube covering his mouth and pumping something into his body, as the walls start to leak the same yellowish-orange fluid slowly fill up the pod. During the same time, the flesh completely encases the now screeching maggot, and slowly absorbs it into it’s mass.

(Hoping something will develop from this. I'm also trying to figure out how to incorporate the interaction between many many kuo-toan encounter after with their attempt at making artificial gods. Also...BBEG... should it be some kuo-toan arch priest who is made on delusions and ordering people around? Should it be a human religious person, such as the head of whoever excommunicated the paladin, or should some type of form of God be pulling the strings? If that's the case, I'd say either the Creator of Everything who neither wants to abandon nor destroy his creation by hand, but still wants to start anew. Blibdoolpoolp, the god of kuo-toans, or the god of chaos who lost his form during the 1000 year war, who wants to reincarnate on this world to resume destruction and multiverse takeover. (The genasi will be an experiment gone wrong trying to create an artificial vessel and soul for some type of god plot.))

Kuo-Toas generally aren't very powerful, the archpriest included. An aboleth, a star spawn, or a beholder would make a better BBEG.

I think you pretty much have everything you need.  Kuo Toa aren't too powerful but they get a lot scarier when you see they can create their own deities through some kind of mad experimentation/thought construction.  I've run campaigns w/ Kuo-Toa as the bad guys abducting people and then have them awaken literally any monster from the MM as their god that's appropriate for the player level.  Just pick up any monster stats you fancy and re-skin it into some other body.  If you're looking for something more specific I agree with the poster above about using an aboleth or you can play on the Kua Toa relationship w/ Mind Flayers.  Maybe their previous masters don't appreciate their new creations?

I like what you've got so far. As for developing a middle, player's rarely do what you want. Think of the 5 or 6 most likely ways they will try to stop the cult, and form a vague idea for how to deal with each. For the campaign I am running, the players have been sent to collect exotic potion ingredients, and I chose what would be going on in each location. For example, there was a revolution going on near the jungle (with one of the ingredients), and now they have joined it.