Pay Me Bug:
Grif and co. would be on the run from Mavis, who is shooting at them in his battle carrier. They drop into Trade Baron space to try to escape but Mavis shoots the outpost, which blows up. Still they trick Mavis and make it to the planet where they refit the ship and are strongarmed into helping the Alliance steal a piece of tech from the Radiant Throne. As they leave Tylaris Prime, Baron Mogra Tylaris is assassinated by the Alliance black ops forces, who blow him up.
Over at Tyrelos Station, Grif and his crew get into a barfight with a bunch of slavers. Instead of being shot in the fight, Grif gets blown up. He wakes up in the hospital and is handed off to the Station Authority guards. They escape by blowing up part of the hospital, but they run into the Sword, who was sent to interrogate Grif. They can't fight him in hand-to-hand combat, so Amys shoots a car, blowing it up.
They finally make it to the planet where they have to steal the thing. They wind up smuggling the thing out of the base by making the robots act crazy. A few of them blow up.
There's a huge chase out of the system -- the Fool's Errand needs to get far enough out of system to jump to tach. Mavis is hot on the trail, and there's shooting. A few ships blow up. Eventually the Fool's Errand escapes by sneaking a bomb aboard the Centurion. The Centurion blows up.
The credits blow up.
Right before Liberty sends off the email, he notices Richter strapped a bomb beneath his desk. he sends the email anyway. The bomb blows up.
CB arrives for the funeral, convinced that Liberty was killed by someone he knew, because not just anyone can blow up Liberty. He investigates the burnt-out remains of the apartment and doesn't the hard drive because it blew up. But as he's looking, he uncovers another bomb. CB jumps off the building. The building blows up behind him. The force of the explosion carries him across the street and he crashes into a balcony on the other side.
CB checks his email, finds the encrypted file, and the bad guys attack the house. That goes pretty much as scripted (I think Bay would actually like most of that scene) EXCEPT that during the fight in the kitchen one of the bad guys is thrown into the gas stove, which turns on, and a few minutes later the spark from a bullet ricochet makes the house blow up. Fortunately the Forrest's were in their safe house.
Plague's power isn't to inflict people with disease, it's to make them into walking bombs. The scene where he blows up his family is probably not going to be as poignant as the original. The scene at the end of year one where CB and Plague fight is going to be Plague trying to turn CB into a bomb, but CB keeps ducking just in time and his neighbors get hit instead.
Also, Plague's name will be changed to, uh, Bomber. I guess.
Year Two: Year Two is focused more on the revelation that magic is involved in this dark plot, but I think in Bay's version it'll be focused on people blowing up. Artemis LaFleur and David Bernard go back in time to the island of Esperanza in order to keep it from blowing up. At the end, everyone attacks a bad guy research facility in Farraday City that has, among other things, a big magic robot that can explode and reform its body over and over again.
Year Three: The heroes (and their villain allies) learn that the master plan is to release a virus that will make every male superhero blow up.