The cycle of flux continued. Plasma splurged together and became energy, then condensed back into matter and antimatter. As this continued, the plasma soup spread further and lost some of its hot hot heat. It only took a fraction less warmth and a bit less excitement for the Quarks and Antiquarks to start to respond to the binding calls of the Strong Force.
The Gluons of the Strong Force bunched the quarks together in big bundles (the antiquarks did likewise). In doing so they formed the first Protons and Neutrons (and anti-protons and anti-neutrons, of course), which are the components that make up the centre of atoms (yep, and anti-atoms too).
The universe calmed down by yet another degree, and the rules of the dance changed once again. Now when matter and antimatter met and dissolved into energy, there was not enough leftover power for that energy to be converted back into matter and antimatter. So the newly formed armies of Protons and Neutrons were suddenly in a battle to the death with the recently formed armies of Anti-protons and Anti-neutrons. This time when they collided, they disappeared forever. The numbers on both sides rapidly dwindled.
Electrons and Anti-electrons formed a little while later in the plasma soup, and went through the same process, annihilating each other, almost to extinction. Almost.
If the universe had been perfectly symmetrical, this would be the end of the story. Matter and antimatter would have entirely dissolved each other in a fizzy flurry and that would be that. There would have been no suns, no planets, no moons, no teacups, no life, no kitchen sink, no nothing. But there was a quirk. A slight imbalance, an asymmetry which for some reason favoured matter over antimatter by as little as a billion to a billion-and-one. And so it was that after this epic battle, a small portion of matter survived that had no antimatter to collide with, because it was pretty much all gone. It is this surviving matter that now makes up every physical thing in the universe.