Following the events of the movie, season 3 follows up on the war of the two sides - now no longer restricted to Earth - the Autobots being led by the self-doubting Rodimus Prime and the soldier Ultra Magnus, while the Decepticons' leader Galvatron now rather deranged and more than happy to club his friends with his fusion cannon, the two sides practically lived though their darkest hour all the time now. However, the ruthless five-faced beings, the Quintessons, are revealed to be the creators of the Transformers, and now attempt to destroy the entire race, manipulating the Decepticons and others in a mad attempt to wipe them from the face of the universe, using such schemes as reviving Optimus Prime as a disorientated zombie and promising the Decepticons a Matrix of their own, they stop at nothing to dispose of the shape-changing robots.
Ultimately, this can leave a viewer rather confused as to what's going on.
Bumblebee, Jazz and Cliffjumper may have survived the movie, and the season 2 combiners and Minibots are still active, but there's really no one for the audience to be familiar with. Jazz is restricted to cameos what with Scatman Crothers' death, and Cliffjumper is entirely absent due to Casey Kasem leaving after some disagreements in racial representation, while the Minibots appear only rarely, leaving the combiners to be the only consistent familiar guys. And the Aerialbots are dicks, so how can the audience use them as a guide to the universe?
In a realistic story point-of-view, this is understandable. You can't fight a war and have all your favourite people survive all the way to the end, and it's only natural for such fights to be taken seriously, but it means that we can't have Rodimus and Magnus lay out an attack plan on the Decepticons only for Huffer to come in and say "you're wasting your time, we're doomed!" and end up taking part. To put it simply, with the darker mood of the series it focuses more on the revelations of their race's past, the pressure Rodimus experiences as successor of Optimus Prime, and about three episodes dedicated to characters nobody likes, rather than as a children's cartoon show point-of-view, which is more about silly storylines that are there to work in characters and make their personality quirks more likeable to an audience to encourage people to buy their toys. Maybe.
This doesn't mean that I think it's bad; in some ways, it's superior than the original series, with the adventures now expanded to the entire universe it allows all kinds of strange people and places to be seen, such as the planet of crazy monkey psychiatrists that use space ants to eat the brains of their patients, or the planet where the creator of Unicron and all his other super powered creations reside; it's certainly a bit more captivating than yet another energy generator building for energon cubes to be made with. The story telling, although still with the occasional dud such as the five part introduction (it's not so much the story that's bad, but more the sluggish pacing and the fact that it just confuses one more than eases them in to all the new characters and concepts), features some utterly fantastic episodes, such as the reluctant alliance between Autobots, humans, Decepticons and Quintessons in The Killing Jar, the diabolical cooperation between Starscream and Unicron in Ghost in the Machine, and the heart rending return of Optimus Prime in Dark Awakening.
The downside is that the animation is wildly inconsistent; sometimes you'll get good stuff that has no real errors, and then there are some that are really just twenty two minute errors with a bit of decent stuff mistakenly put in there. The series does end with some really beautiful artwork that almost rivals the movie in terms of shading and overall great design, and does make up for some of the weaker stuff, but people just love to to cite Carnage in C-Minor as the standards of the season.
The season certainly isn't perfect; sometimes the story is focused on so much that new characters are thrown in with no introduction as to who they are or what they do, and then sometimes more characters are thrown in with elaborate introductions that the story gets muddled behind who the new guy is, but sometimes it just tries to tell a story without commercials involved, and those are where it shines. One could go on and point out the errors and suggest how it could've been better, but it's all done and dusted now, so what good would it make? It's flawed, but it's enjoyable, and I say check it out. Now get your noodle out of my face!