Basically, only a few months after the events of The Dark Side Strikes Back, Luke is captured by one of Sideous's Inquisitors and taken to a remote facility on the Outer Rim for a secret experiment.

Vader quickly catches wind of this and heads there immediately, blasting his way through the base, not caring how angry Sideous will be at him for doing so, knowing how much danger his son is in.

He finds Luke alive, but chained to some strange altar with advance technology pulsing around it. He has no idea what the hell the machinery is it for, all he cares about is getting Luke out of there fast as possible.

Of course the two banter at one another, especially when Luke realizes Vader is rescuing him, his relief flooding the force like a wave, which surprises Vader greatly as they settle into an uneasy truce.

The chains seem to resist to bend under the will of the Force, so Vader is forced to use his metal hands the break them loose from his son's form, but it's too later, the machine activates and they're both seized by a violent, twisted energy.

For a moment all they feel is pain, Vader doubly so as he feels wires and tubes rip themselves from his body as the foreign machine explodes and sparks around them, and then nothing.

When they both regain consciousness, they both realize they've been de aged by almost 10-12 years, thankfully their are memories intact and Vader's lungs and body have healed, but his metal limbs remain, and Luke is now stuck in the body of a small, defenseless young boy.

After a long talk they both agree Luke is too vulnerable to go back the Rebellion and Vader can't go back to the Empire without endangering Luke, so their only solution is to go on the run until they can find a way to get Luke back to his original age.

((They find a way, but it takes like 5 years for Luke to grow back into his twenties. They have to do this slowly with a mixture of medicine and the force because if they try and age Luke too fast is body would go into shock and die.))

((Luke quickly realizes his is essentially holding the leash of the galaxies most dangerous monster. His father would fight anyone or anything for him, and Luke is both overwhelmed and deeply touched by this fact.))

((Luke still has his memories but he still is affected by his tiny bodies hormones. He's physically weak, cries easily, and instinctively seeks comfort from his father, much to his embarrassment.))

((Vader is having a rough time. He's trying his best to behave for Luke, but he feels like he's wearing another man's skin. He can't look at his face in the mirror and usually covers his lower face with a cloth or scarf, as he can't stand how expressive his face can get it either.))

“Being a Sith,” Vader answered. “Like I say, I’m new to it, and you’ve met, uh… I think three other Sith? That I can think of. Darth Maul, Darth Tyrannus and Darth Sidious. So… you know, how am I doing?”

Nute considered his options as to how to answer that.

And keep his head.

“...Darth Tyrannus was usually quite good at running the Confederacy of Independent Systems,” he said, carefully. “Darth Maul mostly caused us a lot of problems. Darth Sidious… has always been good to deal with.”

“Huh, really?” Vader asked. “I’m surprised you think that after he got you arrested.”

Nute blinked.

“He did what?”

“Yeah, turns out he was Palpatine,” Vader explained. “I’m still sort of processing it myself, it has been a hectic day since the fight with Tyrannus.”

“Um,” Rune Hako said, involuntarily.

“Dooku died at least four days ago,” Wat Tambor noted. “It has been hectic for us as well, but I am quite sure of that.”

“Really?” Vader asked, frowning. “I don’t remember going to sleep in that period, but I guess I’ll take your word for it.”

“Sidious was Palpatine?” Nute asked, somewhat in shock. “That – that – all Sith are duplicitous, double-dealing kriffers!”

The shout echoed in the room, then died away, and Nute swallowed.

“I guess,” Vader said, thoughtfully. “You know, he did send me to kill you, so that does track.”

He scratched behind his ear with the hilt of his lightsaber. “And I guess he told me to kill Dooku, you know, Tyrannus, so that checks out too… but… actually, he even hinted it to me with that story about his old master. I think it was his old master. It was definitely about a Sith… and he did betray, like, the whole Republic and the Jedi Order and stuff…”

Nute didn’t say anything, because he felt rather like he was on top of a volcano that might be about to erupt.

On top of, well, the actual volcano he was already on top of, that was.

“...so,” Vader said, slowly, clearly thinking as he spoke. “If the way a Sith works is by betraying people, especially other Sith, because – yeah, I guess that’s a thing that my new boss keeps doing… how do you guys feel about working for me, instead?”

“That sounds like an excellent idea,” Nute Gunray declared.

“Your insight is marvellous, Head of State,” Wat Tambor declared.

“Sorry, is this actually happening or-” Shu Mai began, then Wat elbowed her so hard she fell over.

“...is she all right?” Vader asked.

“She is fine,” Wat said. “What would you like us to do, Head of State?”

“Well, uh,” Vader began, clearly engaged in deep thought. “So… the war was kind of dragging on for ages, but all the Jedi are dead now and I’m pretty sure that the Jedi were a lot of how the Republic was fighting the war. You guys do still have massive droid armies, right?”

“Smaller than they were,” Nute admitted. “We were slowly losing the war. But, as you say, the Jedi are all dead.”

“Then I’ve got a great idea,” Vader said. “Because, uh, I suck at politics but I’m pretty good at fighting wars, so… what about if we make Senator Amidala the Head of State? Then she can make the government be whatever she wants it to be, and I can be the Supreme Martial Commander of the Separatist Droid Armies, which is more my sort of thing. I’m good with droids!”

Nute definitely did not want to give his first visceral reaction to that idea.

“Are you sure she’s qualified?” San Hill asked.

“Of course!” Vader replied. “She’s – oh, hey, I just realized I can actually say it now. She’s my wife.”

The Executive Separatist Council exchanged looks.

The looks mostly involved the tradeoffs between accepting Padme Amidala as their Head of State, and the complaints department of the Supreme Martial Commander of the Separatist Droid Armies.

This might be a new Supreme Martial Commander, who found it much easier to breathe than the old one, but his complaints department was still a lightsaber.

“Excellent plan, Supreme Martial Commander,” Nute said. “Are there any other changes you wish to make?”