It should begin in keeping with the original, with an opening narration by Optimus Prime, explaining that it's now two of Earth's years later since Megatron and the Decepticons were defeated.
In the two years since then, many Autobots have heard Optimus's summons and have already come to Earth. The first real scene of Transformers 2 is a group of "meteors" streaking toward Earth, headed toward a predesignated landing site in the desert of southern Nevada. With cooperation from the U.S. government, Area 51 has now become the "Ellis Island" of the Autobot migrations. We see some of them land, they assume their protoforms and are welcomed by Ratchet (he even gives them a quick examination). The newly-arrived Autobots are then taken to an "assimilation facility" filled with dozens upon dozens of vehicles: cars, trucks, construction equipment, planes. These are transcanned and the Autobots now have their earthly modes.
It is revealed that not all Transformers have the "meteor" capability and that some require more "traditional" descent. Arcee, one of the new Autobot colonists who arrived in the past year, notifies the human Air Force liaison officer that an Autobot "landing pod" is also en route with a group of refugees.
Minutes before the pod is due to arrive though, Area 51 comes under sneak attack in a Decepticon air assault. Yes folks, Starscream has come back and he's brought his friends. Among the attackers is Blitzwing, who astonishes viewers with his ability to transform into a jet fighter and then a ground-based tank.
But the attack is a ruse. A "commando team" of six Decepticons – disguised as construction vehicles – launches a raid on the Area 51 research compound. They are stopped though by Optimus Prime, Ironhide, Hound, Brawl, and Kup. And it's thought that the Constructicons are dead for good.
The landing pod is blown off-course, and crashes further out in the desert, near an outdoor dinosaur museum that's been closed for renovations. We see giant fiberglass replicas of a t-rex, a triceratops, a stegosaur, a brontosaur and a pterodactyl. Five Autobot protoforms stumble out of the pod and in Cybertronian subtitles we see one of them tell the largest of the group that the primary directive upon landing is to transcan Earthly shapes and assume them. The big one, obviously the leader, looks at the t-rex and grunts in subtitles "Me like this one!"
What the Constructicons were after is soon revealed to the audience. The U.S. government, it turns out, has been holding out on the Autobots: years ago it was able to take a sample of the Allspark. The fragment was relocated to Area 51 for further study. Soundwave knew this because it was part of the files that Frenzy hacked from Sector Seven and Frenzy remotely uploaded this information to Soundwave.
Yup, Soundwave has been on Earth all this time, in deep cover and monitoring human communications. And he's already foiled whatever plans Starscream has had for Decepticon leadership by telling the Decepticons that not only does he know where Megatron was laid to rest but that they have a chance to restore him...
...because human scientists have not only kept a functioning piece of the Allspark, but they inadvertently created their own version of the artifact.
I'll cut to the cool part: the Allspark derivative is used in what's supposed to be a "controlled experiment" on the six lifeless husks of the Constructicons. It not only brings them to life but fully resurrects them altogether. They break out and rejoin the Decepticons in time for the big battle at the end of the movie.
But something is wrong: the six Constructicons begin to lose control of themselves and start screaming in their high-pitched language. And then they do something that has never seen before among the Transformers. Something that would have been impossible were it not for the humans meddling in things that they did not understand...
The secondary Allspark has evoked a mutation in the Constructicons. They are about to become an entirely new form of Cybertronian life: a gestalt of their individual bodies.
It doesn't have a name. It doesn't need a name. It's pure brutality and all Decepticon. And it proceeds to unleash holy havoc on the Autobots.
There is a lot more that I've envisioned for Transformers 2 (including Megatron), but you get the gist of it
Bumblebee and Sam find out about the secret Decepticon base in Qatar.
[ Click to attempt signal recovery... ]
