IDW - Alliance

Plot

Four months before the Mission City incident Wreckage is found and taken to a Sector Seven facility where he is worked on by Professor Vine and Agent Salazar to see how the Transformers work.

After the battle in Mission City, the Autobots and Army guys hunt down and kill the Allspark Mutations created during the battle, and Ratchet fixes Bumblebee's legs, which were blown off during the battle. Bumblebee's voice was fixed by the Allspark during the battle. The Auotbots find a trailer to take Jazz's dead body away from the battle site so he won't be taken and just dumped with the Decepticons. The Autobots drive away before mosre humans arrive.

Simmons arrives at the site and they start taking in vehicles affected by the Allspark and the dead Decepticon bodies, Lennox and Epps are consripted into Sector Seven by Simmons. The Decepticon bodies are taken to a Sector Seven base, where Vine learns that Wreckage won't wake up since Salazar went missing (thanks to Starscream).

A month later, Lennox and Epps are asked to get the Autobots to help S7 to escort the bodies of the Decepticons from the base to the docks, ready to be deposited in the depths. Barricade spies on the meeting and contacts Starscream, who is still on Mars after killing Dreadwind.

A short while later the Autobots arrive at the base and begin their escort roles, Optimus looks over the dead body of Megatron and the shard of the Allspark that he removed from his chest after the battle begins to react. Optimus gives the shard to Vine for safekeeping, in case it revives Megatron.

The bodies are transported with the Autobots in tow towards an aircraft carrier for their later departure. On Mars a shadowy figure looks over the remains of Dreadwind and learns of the recent events on Cybertron, but doesn't care, and looks towards Earth for the next clues in his mission.

In Nevada. the Shard is taken underground, and shoots off into Wreckage's chest, waking him up and he starts rampaging around the base, the Autobots are returning from their mission at the same time.

Wreckage breaks out of the base and starts trying to find Megatron, he is attacked by several LM Units from the base, but he easily kills them all, during the battle Vine is killed as well.

Starscream arrives on the scene, and fights with Wreckage as punishment for his betrayal, during the battle Frenzy's head is dropped on the floor and forgotten. Bumblebee and some of the army guys arrive and join in the fight, Starscream kills Wreckage and uses him as a shield and then blasts Bumblebee, shattering his voice box once more, before he can finish him off properly, Starscream is contacted by someone offscreen, Starscream's shocked as he thought he was dead, and flies off to meet up with him. 

Shortly afterwards several Decepticons arrive on Earth in various countries, beginning a search for something.

After the fight in Nevada Simmons is stripped of his command and Sector Seven is finally disbanded after their actions recently and Lennox's team start to answer to a higher authority, Simmons takes Frenzy's head with him and leaves. The Allspark shard is found and Optimus takes custody of it again.

Within 2 weeks NEST is formed, and one of their first jobs is the depositing of the dead Transformers, including Jazz in the trailer. The Autobots and Humans start working together and sharing information as part of their Alliance.

Across the planet the Decepticons start small attacks and take on local alternate modes to aid them in their search mission. Dead End and Swindle are sent out to San Francisco to act as a distraction to the Autobots.

The Autobots and Humans train on Diego Garcia where NEST's base is set up, and the Allspark sharp is being held in a secure facility. The Autobots have set up a signal beacon near Mission City, calling out to any Auotbots to come to Earth as well. NEST learns of the disturbance in San Francisco and head out to deal with it as their first official mission.

The Auotbots and NEST arrive, and the Autobots are told to stay in vehicle mode to maintain their cover. Optimus quickly deals with Dead End, and Bumblebee has a battle with Swindle, but is forced to go into robot mode to do so, and he defeats the Decepticon. Later Bumblebee is berated for his potential breach in cover when they return to base. The Autobots and Humans think that the Decepticons were looking for something, possibly Sam, so they ship Bumblebee off back to Tranquility to protect him, just in case.

Over time, the Autobots and NEST take on several more Decepticon teams across the world and also gain some new troops from space who responded to the signal.

The Autobots and NEST continue training and working on taking down the Decepticons, who also keep arriving. Soundwave works from orbit searching the world for Megatron and the other targets.

The Autobots pick up a disturbance in Shanghai and set off to deal with it....

Characters

Autobot

Optimus Prime - Truck Cab

Ironhide - Pick Up Truck

Ratchet - Emergency Humvee

Bumblebee - Concept Camaro

Sideswipe - Concept Corvette

Arcee - Motorcycle

Chromia - Motorcycle

Elita One - Motorcycle

Skids - Front of Ice Cream Truck

Mudflap - Rear of Ice Cream Truck

Jazz - Pontiac Dead

Decepticon

Starscream - Fighter Jet

Soundwave - Satellite

Wreckage - Personnel Carrier Killed by Starscream

Barricade - Police Car

Fracture - F1 Race Car Killed by Ironhide

Gunbarrel - Battle Tank Dead

Reverb - Military Helicopter Dead

Overcast - Fighter Jet Killed by NEST

Jetstorm - Cargo Plane Killed by Optimus Prime

Dropkick - Pick Up Truck Killed by Optimus Prime

Incinerator - Osprey Helicopter Killed by Optimus Prime

Swindle - Sports Car Killed by Bumblebee

Dead End - Sports Car Killed by Optimus Prime

Demolishor - Excavator

Megatron - Cybertronian Jet Dead

Brawl - Tank Dead

Blackout - Military Helicopter Dead

Dreadwind - Cybertronian Jet Dead

Frenzy Dead

Mutations

Landmine/LM Units - Military Buggies Killed by Wreckage

"Salvage" - Pick Up Truck

"Longarm" - Tow Truck

Dispensor - Drinks Dispensor Killed by Ratchet

Y-Box Console Killed by Ironhide

Steering Wheel (Mentioned) Dead

Human

Lennox

Epps

Seymour Simmons

Professor Vine Killed in Battle

Agent Salazar Dead

Salani Killed by Jetstorm

Admiral Morshower

Sam Witwicky

Mikaela Banes

Bassman

Sarah Lennox (Mentioned)

Sector Seven

NEST

Notes

• This is set during the 2 years between the first movie and ROTF
• It's also the sequel to Reign of Cybertron
• Optimus dons a trailer similar to his G1 counterpart's and his holo-driver is based on Peter Cullen, his voice actor
• Wreckage's disguise colours are actually the colours used for his repaint toy, Bludgeon
• Simmons gets Frenzy's head in this issue after Starscream used it for his own goals in Reign of Starscream
• The Decepticon reinforcements arriving on Earth can be seen as an evil version of the same scene in the first movie (and a precursor to the Decepticons attacking Earth in ROTF as well)
• Bumblebee's voice box is damaged again, explaining why he keeps using the radio in the next stories as well
• Bumblebee is shipped off to protect Sam after he becomes a potential target
• Sideswipe arriving with the Biker Girls and the Twins would later be shown as a mistake, as Sideswipe arrived separately to Arcee and the others and caused havoc in the process. It's possible that he did arrive earlier and was just sent out earlier to look after them when they first arrive.
• NEST is formed out of Sector Seven's remains here.
• The reason Elita One is back to life and not dead is shown in a later story
• The things the Decepticons are searching for are: Megatron's body, the Allspark shard and the Matrix