Ok I'll do my best to split up my idea of the story in sections, just so we can get an overview

We can try mixing it up and putting all the characters after this rough rough rough draft.
Zerg Mission:
Mission 1 (After the Tutorials and Such): Remaining AshesYou play as Kerrigan and her broods. She is on one of the remainder planets that have not been taken over by the Zerg completely yet. In the breifing Duran and Kerrigan are present, Kerrigan gives you orders to wipe out the remainder Protoss on the plannet. After Kerrigan leaves the breifing room to attain to business Duran speaks to you and asks that you capture 10 Dark Templars (Just kill them Unless you have some cool system) and 10 dragoons for reasons he can't discuss (It's not revealed to the player for the Hybrids, and the Goons and DTs will be preplaced in an area you HAVE to pass in order to destroy the base of the Protoss, to avoid killing them too quickly). During the mission nothing else happens, after caputing the units and destorying the base the mission is over.
Mission 2: DisturbanceYou're summoned by Kerrigan again, this time for investigating a large amount of eletrical energy on a vancant area of a planet. Duran is not present for this mission. Whent he mission starts it'll be one of those "No Building" mission, like anything in Installation Terrain, or Shipyards mission. You're giving some units and kerrigan herself, you travel through whatever terrain you decide finding other broods to join you when you eventually reach a squad of Terran Marines. Kerrigan makes the comment "What would the Terrans be doing here?". After fighting through other squads of Firebats, Marines, Ghosts, etc. Duran comes on the Com. with a message "Kerrigan, there has been an attack in our central base by the Protoss" in which Kerrigan replies "Damnit! How did this happen?!" Duran: "They were under containment since we beleive they hold information of remaining Protoss Bases. However they broke out and started releasing other prisoners" Kerrigan annoyed answers the problem "How could this happen?... Cerebrate investigate the Electrical Energy site, I will respond to this threat."
Aftewards kerrigan leaves in an overlord, while Duran comes in with another one. Duran now helps you out through the rest of the mission. After a lot more squads and situations with units like Tanks or Golaiths, you come to a base who's under control of Jim Raynor. You confront Raynor by simply entering the base, which is vancant of patrols or any units, of course text starts:
Raynor: Damnit! The Zerg have found us, well they won't be here long
Duran: Mr.Raynor, I've heard about you from the queen, what are you doing out here
Raynor: That's none of your buisness Duran.
(You are then surronded by Marines, Tanks, Firebats, Dark Templar, and Other protoss units)
Duran: Hmmm, it appears we might have a problem
Zeratul: Hmf
Duran: Quiet the crowd we have here. Zeratul, AND Captain Raynor? What could we being doing here
Raynor: Enough Duran. Waste them boys, but leave the defect alive.
(Afterwards a battle starts with your units verus the other units, the battle doesn't actually end, because "Victory" goes across the screen seconds afterwards.
Mission 3: Break OutYou are back in the breifing room with kerrigan. Kerrigan explains that Duran made a hole in there ambush for you to escape, but in the process was captured by Raynor and Zeratul. The objective for this mission is to get Duran back. You are dropped off in a space platform area with a base that's moderately pass the beginner level of buildings and units. You're suppose to attack the Protoss base where Duran is and free him. Nothing speical happens in the mission, Zeratul or Raynor are not protecting the base.
Mission 4: AlliancesYou are breifed by Kerrigan. She speaks of a suspsion that Duran will betray her. The mission takes place on another Plannet with Protoss, Zerg, and Terran all fighting for control. As you make your way towards the base on the other side (In the way is Protoss and Terran) you find out that Dark Templar, Marines, AND Zerglins are all waiting at an area and they all attack together. Kerrigan's supscison rises: "Terran and Protoss fighting together is no surprise, but what are Duran's brood helping them for?! Perhaps my investigation is too late, we must hurry". After destroying the Terran and Protoss bases you find Duran and a bunch of Statis Cells. Duran starts the covnersation first.
Duran: Ha ha ha, I knew I couldn't trust those characters
Kerrigan: Duran! What is the meaning of this treason
Duran: Treason? I can not commit an act of Treason to someone I was never alligned with
Kerrigan: Explain yourself Duran, my paitence weakens
Duran: This is beyond you Kerrigan, I suggest heading back and getting ready
Kerrigan: Your threats are meaningless, you are here defenseless and dare mock my strenght?
Duran: Oh I am sure if I was actually here you would be quick to kill me. Until next time, Kerrigan.
(At this moment Duran disappears as it's revealed he was a Hallucnation)
Kerrigan: Damnit. Duran is offically an enemy of the swarm. Now get to work cerebrate, destory these cells, then report back.
After destroying the cells the mission is over.
That's all I have for now

I'll be sure to post more later, how do you like it so far?