Star Trek USS Defiant Story Arc

On stardate 5693.2, the starship USS Enterprise enters an uncharted region of space to answer a distress call from her sister ship, the USS Defiant. Nearing the location, the Enterprise's engines begin to lose power and sensors detect a nearby dimensional fracture in space that seems to be the cause of the energy drain. 
The Defiant appears on the monitor, adrift, and with a strange green glow surrounding the hull. Strangely, sensors show no indication that the vessel is there. There are no lifeforms detected, nor are communications established with the ship. Captain Kirk assembles a boarding party consisting of himself, Dr. McCoy, Mr. Spock and Mr. Chekov to beam over and investigate. Before they go, the team dons environmental suits. 
They arrive on the Defiant's bridge finding the crew all dead; having killed each other in what appears to have been some kind of bizarre mutiny. McCoy makes his way down to the ship's sickbay, but he can find no real explanation for the crew's deaths. He goes to look at a deceased crewman lying on the floor and suddenly discovers his hands can pass right through the body. In fact, the whole ship's physical structure seems to be dissolving. 
As other members of the team notice the Defiant's structure is fading, Kirk orders them to return to the Enterprise. Mr. Scott informs the team that owing to problems caused by the phenomenon, he can only retrieve three of them at once. Kirk decides to remain behind allowing Spock, McCoy and Chekov to return, however his delay causes him to phase away with the Defiant. Kirk now finds himself stuck between two dimensions and floating helplessly in nothingness. Spock rushes to analyze the situation and determines that the Defiant's phasing effect should recur within a few hours. When it does, they may be able to retrieve the Captain if he is still alive. 
Meanwhile, the same dimensional interphase begins to affect the Enterprise and her crew. Chekov suddenly goes berserk and attacks Spock on the bridge, and then more violent outbursts occur between crewmembers. McCoy and his personnel rush to find the cause, but they can only assume that the phasing and violent behavior are connected. The same murderous hostilities that affected the Defiant's crew have begun on the Enterprise. McCoy strongly suggests that they put some distance between themselves and the Defiant but Spock refuses, believing any movement from their position could disrupt the Defiant's position and jeopardize finding the Captain. 
An hour passes, and unexpectedly, a small vessel of unknown configuration approaches the Enterprise. A crystalline being appears on the bridge monitor that seems to be surrounded by radiant energy. The being identifies itself as Commander Loskene of the Tholian Assembly, and demands that the Enterprise leave their territory immediately. Spock apologizes for their intrusion and explains their situation to Loskene, asking they be given time to retrieve their Captain. Loskene agrees to give the Enterprise 1 hour and 53 minutes, and no more. 
The moment comes when the Defiant should phase in again, and Spock attempts to lock onto the Captain; however the ship is not where it is supposed to be. Spock believes the arrival of the Tholian vessel has somehow disturbed the Defiant's position and they have lost Captain Kirk for good. 
McCoy and Spock conduct a makeshift funeral in the Captain's quarters where McCoy plays a recording Kirk made for them just in case he was ever killed on a mission. The somber recording gives the officers their final orders and some words of advice for their future missions without him; especially when he exhorts them to use their constant arguments and different points of view to support and help each other. 
After the message is heard, Spock orders the Enterprise to leave the area. However, in the midst of her private memorial for Kirk in her quarters, Lt. Uhura notices a ghostly image of the Captain, still in his space suit, and floating inside the ship, beckoning for help. Spock thinks Uhura is seeing things and suggests she report to Dr. McCoy, but then Scotty reports catching a glimpse of Kirk in engineering and confirms that Uhura isn't hallucinating. 
Spock rushes to locate the Captain, but Kirk phases out again before he can get a lock. If indeed the Captain is still alive, his pressure suit's life support would be dangerously low and his time is running out. 
By now, the Tholians' time limit has already passed, and right on the dime, the aliens attack. Spock returns fire, managing to disable the Tholian ship, but the maneuver leaves the Enterprise critically low on power and Scotty is unable to guarantee survival in event of another attack. 
A second Tholian ship arrives on the scene, sure to finish the Enterprise off, but instead, the two alien ships curiously "link up" and begin to extend an energy thread between themselves. Behaving not unlike spiders, they begin to weave the strange energy strands, in a sphere, around the crippled Enterprise. 
Spock quickly analyses the "web" filaments and announces that if the Tholians complete their trap, Enterprise will not survive. More reports of Kirk's "ghost" come in from around the ship and Spock tries to lock a tractor beam on him when he appears again. In the meantime, Doctor McCoy has discovered an antidote for the phasing effect by using a diluted form of the Klingon nerve agent, Theragen. 
As the Tholian web is nearing completion, Kirk's image is spotted once more and Spock locks onto him with the tractor beam. At that moment, Spock uses all remaining warp energy in the ship's engines to break free of the Tholian's web during the next interphasing. The burst of energy not only releases them, but throws the Enterprise 2.72 parsecs away and well out of range of the enemy ships. Kirk miraculously remains held in the tractor beam and he is quickly transported aboard where McCoy stands ready to inject him with the serum. 
Kirk makes a full recovery and is keen on learning what happened aboard his ship while he was "away". He was surprised to learn McCoy and Spock worked well together, and a little disappointed when McCoy claims they didn't have time to open their Captain's "last orders" and his words of wisdom had gone unheard.
In the Mirror Universe, an amoral, imperialistic version of the Enterprise crew is led by Captain Maximillian Forrest and his treacherous first officer, Commander Jonathan Archer. Archer has proposed that the ship head into Tholian space, where a mysterious vessel has been captured. Archer believes the ship may contain the technology that would be valuable to the Terran Empire. Forrest, however, thinks Archer is merely trying to seize power, and dismisses the idea. A determined Archer has another plan up his sleeve, however — with help from Major Malcolm Reed and Sergeant Travis Mayweather, he stages a mutiny, taking control of the ship and imprisoning Forrest in the brig. Archer promotes Commander T'Pol to first officer, appoints Mayweather as his personal guard, and takes up with Forrest's lover, Hoshi Sato. 
As the I.S.S. Enterprise approaches Tholian space, the crew captures a Tholian pilot. Phlox takes great pleasure in torturing the creature, who finally gives Archer the information he wants: the exact location of the mysterious vessel. 
In Engineering, Trip and T'Pol work to install a Suliban cloaking device on Enterprise. Something goes wrong, however, and a power overload damages the cloak. Archer realizes it was sabotage, and Reed determines that the saboteur was Trip. Reed tortures Trip using the sadistic agony booth, but the engineer offers no further information. Later, Archer has another realization: the target of the sabotage wasn't the cloak — it was the ship's internal sensors. In fact, the actual culprit was T'Pol, who mind-melded with Trip and tricked him into performing the sabotage. 
T'Pol frees Forrest from the brig and the duo takes control of the bridge. Archer, however, has a surprise for them: he's encrypted the ship's controls, and they won't be released until Enterprise has reached its destination in Tholian space. Forrest is furious, but there's not much he can do — especially when he is ordered to investigate the captured ship. 
Archer briefs the senior staff on the ship: it is believed that the vessel came from a parallel universe via an interphasic rift. What's more, the ship isn't just from another reality — it's also from another time, about 100 years in the future. 
Once Trip gets the cloaking device working, Enterprise heads for the coordinates of the future ship. The ship, which bears the name and registry U.S.S. Defiant, NCC-1764, is being kept inside a Tholian spacedock facility. Forrest sends an assault team, led by Archer, onboard. He tells T'Pol to accompany the team — and to make sure Archer doesn't come back alive. The team boards the ship, which is littered with dead human bodies. Still, they manage to bring the Defiant's systems online. 
Onboard Enterprise, the Tholian prisoner wakes up and starts making a racket . Phlox kills it, but Enterprise's problems aren't over: several Tholian ships are approaching. Using continuous streams of energy, the Tholian vessels form a complex web that completely surrounds Enterprise. As the web closes in on the ship, Forrest tries to fight back, but to no avail. Desperate, he orders everyone to abandon ship. From the bridge of the Defiant, Archer and his team watch in shock as Enterprise explodes with Forrest onboard. 
Moment after watching Enterprise's fiery explosion, Archer and his team are attempting to escape on the Defiant. The Tholian ships try to trap them with their deadly web, but Archer and crew manage to get the Defiant's systems working and use the ship to fight their way out. They also bring the escape pods from Enterprise onboard. Archer and Hoshi peruse the ship's computer for information on their parallel universe counterparts. Archer is shocked to find no mention of the Empire — only something called "The United Federation of Planets." He's also disturbed to learn that his alternate universe counterpart is a starship captain and revered explorer. 
The crew eventually discovers that they are not alone on the Defiant — a strange, reptilian creature known as a Gorn is hiding onboard, and he seems intent on sabotaging the ship. Archer goes after the Gorn and the two engage in an intense physical scuffle. Archer manages to get the upper hand by changing the gravity in that particular section of the ship and shoots the alien. 
Later, the Defiant saves an imperial starship, the Avenger, from a rebel attack. Admiral Logan Black, who is in command of the Avenger, is shocked to see Archer at the helm of this futuristic, alternate Earth vessel. Black tells Archer he will recommend him for a command as soon as possible, but Archer is impatient. Tormented by mocking visions of his more accomplished parallel universe counterpart, Archer becomes enraged. He's determined not to let Black take the Defiant from him. His megalomania and paranoia building, Archer shoots and kills Black. He then brings the Avenger's crew under his command and tells them that he plans to seize control of the Empire. 
At least one person isn't sure of this plan, however . T'Pol believes that Archer will use the Defiant's advanced weapons to completely wipe out the rebellion, including thousands of Vulcans. She approaches Avenger crewmember Soval with a plan of her own — she wants to steal the data on Defiant's engines and tactical systems, give it to the rebels and destroy the ship. The duo manages to recruit Phlox and other non-Terrans to their cause. 
T'Pol is found out and taken prisoner, but Soval manages to get control of the Avenger while Phlox sabotages the Defiant. It's all for naught, however — Phlox is taken down before he can complete his sabotage and the Defiant destroys the Avenger. 
Later, onboard the Defiant, Archer and Hoshi celebrate. Archer plans to erase the ship's historical database, to prevent information getting out on the alternate universe. As Archer toasts his imminent reign as Emperor, he suddenly finds himself gasping for breath. He realizes that Hoshi has poisoned him. As Archer takes his final breaths, Hoshi reveals her co-conspirator: Mayweather. The two kiss passionately while Archer dies. 
Now in command of the Defiant, Hoshi orders all to surrender to Empress Sato — the new ruler of the Terran Empire.