Time War of the Main Universe:
The Beginning.
CHAPTER.
Omega screamed, holding his head, as did every other Gallifreyian on the planet. Most falling to the floor, and seizing. The pain was uncomprehensible, as if the universe itself shattered apart.
He could feel it, every single moment, simultaneously under attack. Entire planets being erased from existence.
Her Mate, the great Rassillion, struggle to lift his gauntlet, from his place on the floor. Snapping his fingers, the Gauntlet, one of the most powerful magical focuses technology ever produced, lashed out a wave across the planet.
With it, the screaming stopped... no, it was still there. The universe was still shrieking in pain, but it was just muffled noise to the Time Lords...
Rassillion had blocked out their sensitivity to time. They could function, but the universe was still in incomprehensible pain... still dying... and without their future sight... how would they know how to save her?
Omega was determined to do just that. With a gasp, he stood, while still troubled by the Phantom Pain in his head. He didn't even take a moment to catch his breath, simply running out the room.
He got to the War Room, first. Though Rassillion was only a few meters behind. He was helping the Generals to their feet, when her mate walked in.
"Report!" Ordered Rassillion, the moment he caught up. To which Omega shot him a glare, telling the man to wait a few minutes. That way the Generals could get themselves in order, as well as actually check the readings their computers collected.
"It's the Daleks!!!" The General growled in frustration. "They've rediscovered how to travel in time."
Omega froze, before exclaiming. "How is that possible!?"
"The Doctor took his eyes off them," The General informed. "It gave them time to regroup."
Rassillion scowled, "One man should not be our sole defense against a threat as large as the Daleks. As far as I'm concerned, this is your fault." He accused the general.
Omega eased, "It doesn't matter who's fault this is. We need to come up with a plan to get the Daleks under control."
Skaro.
The Path Web, the cybernetic hive mind of the Dalek race. It allowed the squid like Daleks, trapped in their travel machines, to record and transmit all information they gather.
This "Path Web" doubled as a means to keep information straight, due to the confusion caused by Time Travel. It insured all Daleks, within every time period, could coordinate their attacks.
However, at the height of the time war, the 9th Doctor found out how to hack into the Path Web. He sent his consciousness back in time, to the War Doctor, and did a master delete on all Dalek knowledge of time travel... even sent a command for all time travel devices to self destruct.
The Daleks were able to lock him out... but not before he sent a "Self destruct" order to all dalek travel machines. In one fell swoop, the Doctor not only committed genocide, thereby winning the Time War, but ensured the survivors couldn't undo it. A handful of Daleks were stranded in primitive Time Periods... but most simply died.
They had lost the secrets of Time Travel, with the Valeyard keeping it from them, although he never managed to hack the Path Web again. Thanks to the added firewalls, encryptions, and advanced protections.
But the Daleks saw a moment of hope, When the Clara Doctor. The last Doctor, sent her conciousness back in time, again. This time to stop the 12th Doctor from becoming the Valeyard.
When the 12th refused to accept his army, from Missy, he left the planet with Clara, all business as usual. They shamefully continued their adventures, despite the strain it put on the timeline, now that Clara's Time Lord Genes were activated.
With the Doctor's eyes, temporarily off the Daleks... the Daleks managed to rediscover time travel, and send the knowledge to every Dalek that had ever existed.
"This is a glorious moment." The Dalek Emperor spoke to Davros. Over emphasizing each syllable, as all Daleks do. Though he was slightly more elegant then most. "Perfection has never been so within our grasp.
"If we act quickly, all futures, all pasts, will be erased from existence.
"There will be no planets, polluted with inferior lifeforms, nothing but Daleks in every corner of the cosmos! Once everything is dead, Skaro will evolve in a universe with only one world. A world which will inevitably reach it's perfection, by creating the Dalek race..."
Davros smiled, "As you said, never has perfection been so within your grasp... but there is still one obstacle in your way."
"Yes... The Time Lords." The Emperor admitted. "They stopped us once before. But if we can destroy their pitiful world, before they get a chance to re-synchronize themselves. Their delay in doing so, proves Dalek superiority, and will prove fatal to themselves.
"Davros, begin upgrading all Dalek Travel Machines to that of the New Dalek Paradigm models. The Science division will oversee the construction of all Dalek Vessels, with weapons capable of shattering solar systems. I will be directing the Parliament of the Daleks, and their Fleet, to Gallifrey."
Davros frowned, "Are you certain this 'Dalek Prime Minister' they have, will relinquish the power over their Fleet."
"Such thinking proves how you, creator, are inferior." The Emperor insisted. "No Dalek would allow their ambition to interfere with the ultimate goal of all Daleks. The Prime Minister will take it as a matter of course that I direct their fleets. I was designed for military precision, at the height of the Time War. I am the best suited for the task.
"Then once all is exterminated, and nothing but Daleks remain, I will step down and allow the Prime Minister to rule in Domestic matters, as he was designed."
Davros smiled, "Of course, I should expect nothing else, from the ultimate lifeform."
The Emperor eyed him a moment, "When the Time Lords are Exterminated, we can turn our army to the rest of the Cosmos. All will be purged, until there is only Dalek!!!"