Hey Rock, I had an idea that you could use for a non cannon story just for fun even if it's just as posts.
You could basically use team's rwby and jnpr from any point from the past, from the beacon days to when they're working with Ironwood and just have Penny go with instead of Pyrrha because she dies at the end of the beacon days and have them travel through your au's. I know I've been on the Arc effect au train a lot but I figured that one would be a good one to start with because it gives the opportunity for a little mystery to be solved.
The group is separated when they arrive. Team rwby is on a remote planet occupied by criminals, and team jnpr is somewhere more public. (I'll let you decide which because of the options available.) Anyways team rwby would have a little trouble getting off world but thankfully for some luck they get help from the rachni and the rachni queen who are traveling around the galaxy. She would then tell them that she knows this au's Jaune but wouldn't say it out right and says his name in the rachni language "Gedeon" (hope I'm saying that right) leaving them with a mystery to find out who he is and get his help.
Meanwhile with team jnpr they would have issues of their own, like being hunted by Cerberus and trying to get some help to find their friends. Along the way they would notice that a lot of people would recognize Jaune which would leave especially him confused. Along the way both groups would get help from people that know the Jaune of this au and would eventually meet him later on.
I've tried to explain this the best I could and I want to leave room for you to add your own ideas for it, but let me know what you think.
I like this idea, but I think the only change I kinda wanna do with this is keep RWBY and NPR together. Also, I will be using Volume 2 RWBY & NPR!
"Where the hell are we!?" Yang asked.
Currently, teams RWBY and NPR, minus Jaune, found themselves in a large cavern. They didn't know how they ended up in the cavern, one moment, they were all hanging out and the next, they ended up in this cave.
"Who knows, but what we need to do is stay calm," Blake said.
Weiss nodded in agreement. "I agree. While it is worrying we ended up in the the blink of an eye, panicking isn't going to do anything,"
Pyrrha also nodded in agreement. "You're right. What we need to do is find away out." She said.
"The question is, which way is out," Ren said.
Ruby rubbed her chin. "Good question..."
Blake opened her mouth to suggest something; however, she stopped and her cat ears perked up and her head turned toward the pathway ahead of them.
"Something's coming," She said. "No, wait... There's a lot of somethings coming our way!"
Quickly everyone grabbed their weapons in case what they come face-to-face with was hostile. Suddenly, what seemed like hundreds of hundreds of bug-like creatures appeared and scurried all around them, and while that made them all feel a sense of danger, that wasn't the weird part.
"Huh!? I thought it was Gedeon!"
"What are they doing here!?
"No... They feel different!"
"Why do they feel like Gedeon?"
The two teams froze as they heard voices coming from the creatures, voices that sounded like people. It made them all pause for a moment, none of them knowing what to do or how to react.
"Please tell me I'm not the only one hearing voices from these things, right?" Nora asked, looking a little uneasy.
"No, I hear them too!" Ruby cried, shocked.
"What... Are they?" Yang asked, also stunned.
Suddenly, the pathway began to shake, as large and more booming footsteps echoed through the cavern. Finally, a larger and bigger bug-like creature appeared, and it towered over them all. It was bigger then any Grimm they had encountered.
"Whoa! That things huge!" Nora cried.
Weiss turned to Ruby with a raised brow. "What's the plan, Ruby!?" She asked.
However, before the young silver-eyed girl spoke, a booming feminine voice spoke.
"Who are you... Why do you feel like..." The voice began, trailing off. "Oh, your songs, your music, they are like Gedeon's with different tunes..."
They all turned to the giant bug, understanding that it was the source of the voice.
"Who are you?" Ruby asked.
"I am Yaawa, Mother of the Rachni and friend of Gedeon," Yaawa replied. "Who are you, little one?"
"I'm Ruby Rose," Ruby replied.
"Ruby Rose... Ah, so you are the one Gedeon spoke so highly of," Yaawa said, her voice sounding more cheerful. "It is too bad he is not here to see you; he has spoken highly of you and those with you."
Ruby's expression turned into confusion. "Who's Gedeon?" Ruby asked.
Yaawa's head tilted, as if confused, before it straightened out again as if in realization. "Forgive me, I forgot you do not know our ways," She said. "Gedeon is the name for him in our tongue; however, for you, he is known as Jaune Arc."
"You know, fearless leader!?" Nora asked, eyes wide.
Pyrrha's expression turned to shock. "Jaune knows you?" She asked.
Yaawa nodded. "Yes, we know each other," She began.
"Where is he?" Ruby asked.
"He is not here, but I may be able to get him here through one of my apostles," Yaawa said. "Please follow me and my children; I promise no harm will come to you."
With that, many of the younger Rachni scurried away with Yaawa following after them. However, a few Rachni approached Team RWBY and NPR and nudged them along like dogs.
"Come, mother is right, you're safe here!" Said one of them.
"Your songs are so different from Gedeon's! They make some beautiful music," Said another.
Another then asked, "Can you tell us stories of Gedeon since you are his friend?"
The two teams agreed to tell stories about Jaune to the young Rachni, all while still finding the situation very, very odd. They followed after Yaawa, guided by the young Rachni who were walking with them. They had so many questions on their mind, but the biggest one was how Jaune knew or even met these creatures.
Meanwhile, aboard the Normandy, the Crew was drifting through space, with Jaune and Shepard sitting at the bar.
However, their moment of relaxation was cut by the sound of Joker of the PA system.
[Um, Commander, is Jaune with you?] Joker asked.
"Yeah, he's with me, Joker," Shepard said.
"What's up? Is Gracie crying?" Jaune asked.
[No, Tali and Jack still got that covered. We received a transmission from one of the Rachni's apostles] Joker told them.
That quickly got both of their attentions.
"What about?" Jaune asked, concerned.
[Uh... Apparently, your friends are on her planet?]
Jaune's bro arched in confusion. "My friends...?" Jaune asked, confused. But then, realization hit the blonde, and his eyes widened to the size of a dinner plate. "RWBY!" He cried.
Shepard looked shocked as well. "You think it could be them?" She asked.
"It's the only thing that makes sense!" Jaune cried. "Joker, can you set a course back to Utuku?"
"Can do, but is SHepard-"
"Do it, Joker," Shepard told him. "If there's even a chance it's them, we have to take it."
[You got it, setting a course for Utuku,] Joker said happily.
Quickly, the ship flew to the nearest Mass Relay, and as it did, Jaune couldn't help but feel a sense of joy and dread swelling up inside of him...