New Universe Returns
I'm a big fan of GUP, and I've just finished (and loved!) Sky Girls. I'm not really sure how to fit GUP in, since it's a game instead of a war. Although the thought of the girl's tank transforming into Warpath is totally awesome :D As for Sky Girls, maybe…. Definitely interesting.

Rei and Akane landed in front of the base's main building. A pair of soldiers immediately led them to a waiting room. Inside were Aoi, Wakaba, and Himawari. Aoi and Wakaba were both standing, while Himawari was seated watching TV.
"Hi guys!" Akane said.
"Akane!" Aoi said.
"Now now, you took all the cool parts again," Wakaba said.
Rei entered the room. "Umm… hi."
"Whoah. Rei! Nice to see you again!" Aoi said.
"Yeah," Wakaba said. "Are you staying this time?"
"I'm not sure," Rei replied.
"Well, we should hang out once we get the chance!" Akane said.
Wakaba turned to Himawari. "Hey, Himawari! What are you doing?"
"Scanning channels," Himawari said.
On the TV, a reporter was talking.
"…. Serial killer, known as the 21st century Jack the Ripper, has been recaptured…"
Himawari changed the channel.
"…American inventor Joshua Joyce announces…."
Himawari sighed and turned off the TV.
"It's not on the news at all. Strange. Back then the Alone attacks were front page news. You'd think this one would end up in the front page too."
"That's NEST for you. They can cover things up pretty fast."
All five of them turned to the newcomer who had just entered the room. She was a brown haired girl who wore eyeglasses.
"Hi. I'm Shiena, and I'm NEST's contact in this base."
"So, you work for them?" Aoi asked.
"If you could call it that."
"But I know you!" Akane said. I saw you on your first day here. I remember Grandpa praising your computer skills."
"Those were the same skills that impressed NEST," Shiena replied.
"You don't seem to be the fighting type though," Rei commented.
"Yeah, I'm not. They recruited me after I got kicked out of school. It's… a long story. Either way, the Autobots are ready to meet you now. You can go to this base's runway."
"Alright! Thanks, Shiena!" Akane said.
The brown-haired girl watched as the five exited the room.

"Wow! Check that out!" Aoi said, amazed.
In the runway, a huge C130 plane can be seen. It's door was already open, and vehicles can be seen disembarking. First was a gray delivery van, followed by a small black motorcycle. Already on the ground was a silver sports car. A huge blue and red truck was next.
The truck transformed, its parts shifting.
"Amazing, isn't it," Lennox said.
The girls just nodded.
Finally the transformation was complete. The tall robot stood over them, staring at them intently.
"Hi!" Akane said.
The robot paused. "Hello. My name is Optimus Prime. I am the leader of the Autobots. I would like you to meet my comrades"
He pointed to the delivery van. "Rollbar."
The van transformed. "Nice to meet you, girls. I hope our alliance works out well."
The motorcycle transformed. "Hi girls."
"Sideswipe, who has been here already for some time…"
"Sorry that I wasn't able to do much in the battle earlier, Optimus," Sideswipe said.
"We all have our limitations, Sideswipe," Optimus replied.
"And I take it you are already familiar with Breakaway?"
As if on cue, the brown jet descended, transforming as he landed.
Nice to meet you girls!" He turned to Akane and Rei. "Great fighting back there," he said, giving them a thumbs up sign.
"Thanks!" Akane replied.
"So, why are you here? " Rei asked.
"We are here to protect your Manifestation Engine from Megatron and his evil Decepticons," Optimus said. "Like us Autobots, they can also transform. I have been informed of your capabilities, and Breakaway here can attest to your strength. But this is not something you can do alone."
"When are they going to strike?" Wakaba asked.
"We do not know," Optimus said. "You may have heard of a battle in Egypt. It was actually a battle fought against the Decepticons, with us Autobots and our human allies in the front lines. It resulted in Megatron's defeat. However he had survived the encounter, and has been hiding. Your Engine is one of the probable targets he might attack, and with Decepticon activity here it confirms our suspicions."
"What now, then?" Himawari asked. "Do we wait? Or do we find them and attack? I won't let them harm the engine."
"I think it is better for us to stay put," Rollbar said. "We can just wait for them to come to us, so that we can finish them off."
"I see, that makes sense," Wakaba replied.
Lennox spoke up. "I know you all have regular lives. You can return back to your homes for now. However we expect your help once the Decepticons are here."
"Of course!" Akane replied.
"You can count on us," Aoi replied.

"So, there's a new threat, huh," Wakaba said.
"A hero's job is never done!" Akane replied.
"Now, how can you be so cheerful about this?" Rei asked.
Akane flashed Rei a smile. "Because we're all together again! I'm sure nothing can stop us once we work together."
Rei nodded. Akane's cheerfulness and optimism are what she liked most about her.
"Well then, you guys go on," Wakaba said. "Me and Himawari's house is over there,"
"Sure. Bye!' Aoi replied.
"Bye guys!" Akane said.
Rei gave a little wave.
"Say, Rei? Where will you stay?" Akane asked.
"Well… I have not really thought about it. I guess I don't have an apartment anymore, so I don't really have anywhere to go."
"Well why not stay with us?" Akane replied. "It'll be like the time you went over for dinner."
Rei brightened at the thought. "Sure!"

Unseen from the five girls, a white car can be seen watching them. It had no driver. An ordinary passerby would have thought that it was just a parked car, but in truth it was a Transformer. And it was busy transmitting information to its master.

The Decepticon base is located on an island near Blue Island. Thanks to Depthcharge's stealth capabilities they were able to make it so that it would be undetected by human sensors.
"So the Autobots have arrived…" Megatron said. He was facing a console which he uses to communicate with Soundwave. Also in it was the data Deptcharge managed to send out before his death.
"Soundwave! Kindly explain to me why these humans were not mentioned in your report."
"My apologies, Lord Megatron," Soundwave replied. "But all data indicates that the team had gone inactive, and that they are no longer a threat."
"They are now!" Megatron replied.
In the background Starscream waited. Soundwave is pretty lucky he's not here, he thought. The Deception data master was currently in outer space, attached to a satellite. Or else he might be in the receiving end of Megatron's anger.
"Very well," Megatron said. "I hope that this will not happen again. Continue your surveillance!"
Starscream now approached his commander.
"My lord," he began, "I have sent Brakedown to the mainland, in order to scout-"
Megatron gave him a punch in the face. Clearly the Decepticon commander was still angry and Starscream provided him with an outlet to vent his anger. "I am the only one who gives commands here!" Megatron replied.
"But master, it is necessary for us to gain information about these humans-"
Megatron kicked the air commander. "As I told you before; there is no command but mine." He turned to the console once again.
"Brakedown! I want you to report your findings to me. Finding information on those girls is of importance."
Over the intercom the Decepticon's scout's voice can be heard. "Yes sir."
Shockwave entered the room.
"The first is done, my lord," he said.
"Excellent," Megatron replied. "Be ready at any time, Shockwave. I may call upon your creations to do battle."
"Of course, sir."
Megatron stared at the console again. It displayed a view of the manifestation engine. He had failed too many times. But he will not fail again.

The bots mentioned here are:
ROTF Rollbar
ROTF Knockout
ROTF Brakedown