everal plot points were added during TFG2 that are important to the 
continuing story. These were:

1. During the four million years the Autobots and Decepticons lay 
deactivated on earth, a new army of Decepticons, more dangerous and 
merciless than the others developed, evolved, and left Cybertron to 
colonize planets, inhabited or not, in Cybertron's image.  Any 
inhabitants were killed; the planet was covered in metal and any 
ecosystem was destroyed.

2. This second generation of Decepticons discovered a lost bit of DNA 
and programming that allowed them to go through a process of binary 
replication, were one TF could split in two separate organisms.

3. The replication process degraded the morality in each new 
generation produced, which is why Optimus believed that Primus stopped 
their ability to do this replication. The replications of the newest 
generations produced an energy called the Swarm.

4. The Swarm was somewhat intelligent, and more dangerous than the 
second generation Decepticons could ever be; it could not be destroyed 
due to it being a type of gaseous energy with no true form. Parts 
could be destroyed, but it would regenerate as soon as it was hurt. 
It could consume the matter in bio-mechanical beings of any kind,but 
would not consume just biological beings like humans. Applying 
rheanimum to metal renders it superdense and impervious to damage, 
and is therefore the best defense against the Swarm.

5. The matrix is part of Primus's lifeforce that he used to activate 
his army. The holder can use it to bond with anything around him, can 
manpulate matter, and use its excessive power to do nearly anything 
the user desires.  Unfortunately for any Decepticon, the matrix holds 
the ability to control the one trying to control it. Optimus always 
used it in a sort of symbiotic relationship. When someone who doesn't 
follow Primus's belief gets ahold of it, it rewrites their mind so 
they do. 

6. Megatron stole the matrix from Optimus and used it to activate the 
Rotor Force and the Laser Rods. They battled the other Decepticons and 
were defeated.

7. Autobots and Decepticons allied together to fight the 
second generation Decepticon army.

8. Starscream took the matrix and used it to bond with the War World 
spaceship. After a certain amount of time, he felt the need to defend 
the earth from the second generation Decepticon army, and he realized 
that it was changing him. He gave it back to Optimus before he could 
be turned into an Autobot.

9. The Swarm was changed by the matrix into a force of life, after 
consuming the entire second generation Decepticon army attacking the 
Autobot/Decepticon army on earth. It consumed Optimus and released 
the matrix's power.

10. Two of the Rotor Force switched sides, and Darkwing was changed 
into Dreadwing.

These are some of the more subtle parts of Generation 2 that are 
important to the overall plot of future stories involving the original 
army.