Unicron flies off towards Cybertron. More on that plotline later.
Galvatron and his minions show up on the Planet of Junk (Unicron told them where to go -- otherwise, as is typical with Decepticons, they would have simply flown around bumping into walls for the rest of the movie). There they encounter Ultra Magnus, who you might recall was given the Creation Matrix by Optimus Prime. Galvatron and the Sweeps (those things that look like flying submarines) defeat Ultra Magnus and run off with the Creation Matrix. This is intended to be tragic, but it doesn't really come off, partly because the battle with the Junkions intercedes.
One more cynical point about toy manufacture -- it's much more profitable to produce one item in large volume than several different items in smaller volumes. If you can convince kids they need to buy three or four Sweeps, all identical, you triple or quadruple sales volume without paying for the extra manufacturing overhead of actually making different toys, or the scriptwriter overhead in writing multiple characters. Hooray for capitalism.
The battle with the Junkions is a sort of mutual crotch-sniffing event with the Autobots -- they have a fight in which no one gets hurt, then reach a stalemate, then Peace is Made. Right then someone cranks out the Universal Greeting. Unlike the Sharkticons, the Junkions are not minions of anyone nefarious, so it works nicely, and gives way to the most undiginfied scene ever to appear in any Transformers outing, where the Autobots and Junkions end up dancing around a fire to Wierd Al Yankovic's "Dare to be Stupid." I have no idea why this didn't wind up on the cutting-room floor.
Having captured the Creation Matrix, Galvatron flies back to Unicron (again), this time attempting to get the better of Unicron by bluffing about the power of the Matrix (sofar the power of the Matrix consists of emitting blue light). By way of response, Unicron transforms from planet to robot form (invoking the Always a Bigger Robot principle) and eats Galvatron. He then runs off to attack Cybertron. Cybertron, you might recall, was in the hands of the Decepticons, so there follows a battle between Unicron and the Decepticons, with the ever-loyal butler Shockwave leading the defense. The outcome isn't particularly clear.
Unicron abruptly acquires the ability to breathe blue fire, which he proceeds to do at the Junkion spaceship which came along to the battle. This part doesn't prove a problem for them, but a moment later Unicron catches hold of and crushes the Junkion spacecraft, thus eliminating the Junkions from the brief list of surviving characters.
Also some parts of Unicron prove to be full of water, which suddenly starts flowing around and threatening to engulf various Autobots.
At about this stage, a captured spaceship containing Hot Rod, Kup and the human Daniel flies into one of Unicron's eyes so they can go battle the swallowed Galvatron. Daniel comes across a bubbling vat of something hot and acidic, over which runs a cable responsible for dropping various characters eaten earlier in the movie into the acid vat. These characters include Daniel's father Spike, whom he miraculously saves by the expedient of knocking down the cover over the vat. By implication, he also saves the three other Autobots eaten earlier in the film (Jazz the Porsche, Bumblebee and Cliffjumper the VW Beetles), but we only find that part out because they flash by the screen briefly a few minutes later.The Climactic Ending, The Less Climactic Rising Action, The Spinoffs