The overall arc in the third season was mostly a diversion, setting up another Goa’uld as the main villain (Sokar), only to let Apophis return to power and reclaim all of Sokar’s dominion. Though, it wasn’t exactly a big plan by Apophis, but purely happenstance. SG1’s attempt to stop Sokar, who became powerful enough to overthrow all the other System Lords, worsened the situation by merely killing Sokar and allowing Apophis to pluck the ripe fruit that were his belongings. By the way, Sokar reminded me of the prior, the servants of the Ori in season nine to ten. Maybe the reason he managed to marshal such vast resources in such a short amount of time was due to an outside source.
Like in the first two seasons, the format hasn’t changed much. Self-contained single episodes and continuity heavy episodes. As with all TV-shows that have such a mix, sooner or later the single episodes suffer in comparison to the continuity-heavy ones. Even a weak of the latter is more interesting than a well done single episode, because when all is said and done, a story that spans a whole season or more always feels more important than a story that can be finished in under an hour. Even if objectively speaking the overall arc isn’t all that good, it’s delivery makes one crave the next piece of story instead of maybe a superior but self-contained and finished episode. That said, apart from Urgo and A Hundred Days, the other self-contained episodes were largely weak this season.
One thing about StarGate I found less appealing was the way how they handled the Tollans. They were reintroduced as a plot element in Pretense, and it got from bad to worse each time they appeared on StarGate, until their complete annihilation in season five. I always got the feeling someone on the writers crew hated how they acted in their first appearance and wrote episodes like Pretense and the rest to reestablish the superiority of humanity over everything else (yes, no one on the show thinks like that, but theres an implicit element to StarGate that Earth’s humans are superior, like in most old-school space opera). As if someone really resented to be handled like children (season one: Enigma) and this was his revenge. Pretty petty if you ask me.
That said, one highlight of the whole season was the introduction of the Asgard enemy, the replicators. They are IMHO one of the greatest inventions of the StarGate universe, not because they are original in a thematic sense, but because they are the best visual representation of the idea of gray goo I’ve ever seen. Yes, they are not nanotech, but while nanotech works well in written fiction, in a visual medium you need something more, well, visual. And oh boy they are. Like LEGO toys run amok. Brilliant, whoever designed them.