I know you guys have them and there are probably threads about this, but hey, sometimes ya got to start fresh to show you want it.
T1: 5 mission arc where you discover that a high ranking KDF member is Undine, but you do not know who.
You are on a standard patrol in Nawlogh system when you come across a Gorn ship which should not be there. An escort warps in, you start attacking but the gorn captain takes a litle too long before he helps. You hail and board the Gorn ship. You talk to the Gorn captain - he said something weird and gets you thinking. You leave but in a manner that allows you to get a DNA sample. The Gorn ship warps out. You warp to Saqghom system to continue your patrol.
You scan the DNA and learn the Gorn captain is Undine. You report this to your superior who'll get back to you. In the Saqghom system you find an Undine ship in orbit and get a distress call - beam down and fight Undine and help secure the facilities. When the fight is over, there is an Undine survivor - barely a survivor - with information that high ranking officials in the Empire and it's allies are Undine spies - the Undine is no longer a survivor.
You continue your patrol and start heading to the Hedon system. On route you receive a message to avoid the Hedon system and proceed to the No'mat system from General Whomever. When you get to the No'Mat system and find some Gorn, Romulan, Nausicaan and KDF ships - empty ships. You are ambushed by Undine ships. After defeating the ships you beam down to the planet because of a strange signal. You find Romulan, Gorn, SF, and Nausicaan prisons. You fight the Undine and free the prisoners. One of the Gorn prisoners is the captain of the Gorn ship from part 1. He tells you how he was rerouted to the No'mat system, boarded, and was taken prisoneer.
After talking to the Gorn captain, you decide that the Hedon system needs to be investigated. Once you get to the Hedon system, you fight large waves of Gorn, Nausicaan, Romulan, and KDF ships. You get to the planet, beam down and have to free prisoners. These are not just any pioneers, they are the captain, BOff's and large numbers of the crew of the I.K.S. Kaarg.
You head to the I.K.S. Kaarg. You are hailed by the Kaarg's captain and told this space is secure and they are on a mission from the high council. You inform them that you have been order to delievre a personal message from General Whomever. You beam aboard proceed to the ready room and confront the captain. You have to fight your way back to the transporter room, then fight the I.K.S. Kaarg with the aid of some Gorn, and Nausicaan ships from the No'Mat System. When you win, the real Kaarg captian and crew are back in charge of the I.K.S. Kaarg with a plan the two of you cooked up to find more Undine spies.
T2: 5 mission arc where you find a high ranking Undine spy in the Nausicaan ranks
You recieve a coded message from the I.K.S. Kaarg, "Nausicaan ship in Gorath." You proceed to the Gorath System and hail the Nausicaan cargo ship, and beam over. You get to the ready room and talk to the captain. Little banter about how he was diverted from the Hedon system and told to wait here for further orders. You depart and grab his DNA.
You scan the DNA and it is Nausicaan. You are about to warp out of the system when engineering reports the Nausicaan ship's warp core is about to breech. You have ten minutes to beam aboard, get to engineering, fight/find all the engineers on the ship are Undine, and stop the breech. What is so important about the ships medical cargo?
The medical supplies are picked up on Ghuh'woq. You proceed to the system, beam to the planet and talk to the production manager. The material is just used for production in a standard Nausicaan child's vaccination, and a fermenting agent in Nausicaan beer - a nasty tasting beer.
You are about to beam up when a Gorn ship warps in and start an orbital bombardment. Your ship, after taking a direct, critical hit, has attacked the Gorn ship and can beam you to the Gorn ship. You beam aboard a Gorn ship, but it is not a Gorn ship. It is a Undine ship. You fight your way to engineering and cause a warp core breech.
You beam back to your ship. The Undine ship does not breech, but it does manage to escape to fluidic space. You chief scientist did manage to upload a virus to the Undine computers, and the data is streaming to the I.K.S. Kaarg. (You hope the plan to expose more Undine works.) The only other clue you have is a Nausicaan captain, Captain Vornmk
T3: 5 mission arc finding Captain Vornmk and the honour of working for J'Vek. (We know from Terrordome J'Vek is Undine.)
You relieve a message from a trusted warrior, blood brother from the Klingon Marines. They have the location of Captain Vornmk, he is the commander of a KDF BoP that is stationed in the Zibal system as a crude listening post. You warp to the system and are engaged by Fed ships.
Once the Fed ships are distroyed, you circle to the far side of a planet and find Vornmk's BoP and a SF escort in orbit. The ships attack. Once they are destroyed, escape pods head for the planet.
Beam down to the planet to kill any survivors that are not useful to you, and one is, Captain Vornmk. The captain changes to his Undine form and you battle till the Undine is captured. Your marine friend sent a BoP, the I.K.S. SwissCh'al'et to help you, but the I.K.S. SwissCh'al'et only arrives in time to take the captured Undine back to Qo'Nos. Your name is getting to be known by KDF - not to mention the Undine.
Command J'Vek contacts you. He sends you Archanis System. He wants you to meet with someone for a secret mission. You warp into Archanis system and recieve a message from the U.S.S. Poseidon. The factory on the planet is producing a chemical weapon that needs to be destroyed. The Poseidon warps out and you beam to the planet.
Instead of blowing the factory up from orbit, and because you don't really trust the Feds, you beam down. You make your way to the factory and find it is another component for the Nausicaan child's vaccination, and a fermenting agent in Nausicaan whiskey. You report back to J'Vek you believe the U.S.S. Poseidon is being used by the Undine - your investigation of the factory yields nothing.
T4: 5 mission arc where your plan to expose Undine spies pays off.
You receive a message from the captain of the Kaarg. He cannot decipher the message yet, but he knows the source is in the Ghomha System. You proceed and start to engage the same Undine ship, this time, the I.K.S. SwissCh'al'et arrives in time for the battle, and what a glorious battle it is. Some Undine escape by beaming down to the planet.
You beam down and battle the Undine. You manage to capture one, and he tells you about the Gorn captain. You give the Undine a good death for his information.
You contact the I.K.S. Kaarg with the name of the Gorn captain. The Kaarg's captain will get the information, but in the mean time, the other source of the data stream is in the ChoS Nebula. You warp to the ChOS Nebula and are attacked, and boarded. You defend you ship to the death.
Once the boarding party has been repelled, you have managed to weaken the Romulan Warbird and decide to return the favour. You board and fight to the captain's ready room and capture him. You take the Undinde prisoner, the only survivor. The I.K.S. SwissCh'al'et takes another Undine prisoner to Qo'Nos.
Commander J'Vek gives you high regards and suggest search the Trealus System for the U.S.S. Poseidon. You warp to the system, but you are meet by a fleet Fed, Gorn, KDF, Nausicaan, and Romulan ships. Lucky you were smart enough to call for help. The Kaarg and I.K.S. SwissCh'al'et warp in to help in a glorious battle. The U.S.S. Poseidan warps in after the battle, and warps out just as quick.
T5: the scary Nausicaan vaccination
You get a message from J'Vek that a Undine ship has been spotted at the Ganada System. But the reports come from a Ferengi traders which means it may not be reliable. You warp to Ganada and meet the Ferengi. He is transporting goods that can only be found in Federation space. The goods are also used in a Nausicaan vaccination and a preservative in almost every Nausicaan alcoholic beverage.
The Undine ship warps in and attacks the Ferengi ship. You attack the Undine ship.
You recieve a message from the Kaarg, the Undine ship you just destroyed sent a message Aldebaran System. You warp to the system and find federation ships in orbit. You attack the ships.
A signal is coming from the planet. You beam down and find a Undine installation. You fight your way to the installation, and come across Captain Sulu. You fight your way to Sulu but he has beamed up to his ship. You beam up and fight the Poseidon. The Poseidon escapes.
J'Vek Summons you to Qu'Nos and wants you to interrogate the Undine prisoner, but the prisoner is to not be harmed. You decide to replicate some supplies first. The prisoner is brought to your ready room. You ask the importance of the Nausicann vaccination, but does not reply. You take the vaccination and nothing happens; you give the vaccination to the Undine and he screams in pain and passes out. J'Vek beams up and meets you in the ready room. You have the other supplies and decide not to waste them. You drink the Nausicaan ale and whiskey while talking to J'Vek, and for one brief second, J'Vek looks like an Undine.
Before someone said, hey you can do this with the UGC, this type of mission would take a very sophisticated scenario editor (UGC if you prefer), and may not be possible.