I was looking all over but couldn't find this. I seem to recall that this might have been posted in the original Scans Daily and as such just making sure that this is restored. As an added bonus I'm putting in #4 in here as well.
Not many scans due to this had a much smaller pages (I think I counted 24). So I limited the pages But they are oh so good ones:
The Autobots send a probe to locate the Dinobots. Accidently alas it revives Shockwave instead. Anyway massive fight between Decepticons and Autobots and Decepticons:
Next issue Shockwave is watching human life via television (make's you wonder what he think of it now with the internet):
As for the Autobots fates after this?
For where Shockwave is marching too? A recovering yet bound Megatron who is none to pleased to see his second-in-command here and taking over his leadership.
The issue ends with the only Autobot not caught, Rachet and human Buster Witwickey arriving upon the Ark to find the new owners. Not soon after Buster make's this horrifying discovery of Optimus's disembodied head telling him he's the final hope for the Autobots.
I only got the next issue with the grudge match between Megs and Shockwave for leadership of the Decepticons, the Constructicons and Jetfire's first appearances, and the conclusion to all this which is give or take was #10-12?. I say ? cause I know it's the conclusion to this all (and Megatron returns next issue), but I don't have the cover. I lost it years ago :(