The argument could be made that the first third was a “slow build”, putting pieces in play that would be needed later. While there is some truth to that (Rajiin introduces the idea of the Xindi working on a biological weapon as a Plan B, and Exile has a B-plot in which a connection between the Spheres and the Anomalies is made clear– but both of those are drops of data in otherwise wheel-spinning exercises.)
So, onto the middle third of the arc, things should pick up? Should, yes. But doesn’t. This middle third batch of episodes are: North Star, Similitude, Carpenter Street, Chosen Realm, Proving Ground, Stratagem, Harbinger and Doctor’s Orders. Of this batch of eight, only three do any heavy lifting in terms of the arc plot, and they’re back-to-back-to-back: Proving Ground, Stratagem and Harbinger. The rest are very mushy mushy-middle stuff.
The two biggest missteps are North Star and Carpenter Street. Strictly speaking, Carpenter Street does do some arc-work, but it’s not compelling. Both these bits suffer from having an “neat idea” supersede what the story arc really needs. In the case of North Star, it was doing an old-school, Original-series style of episode where they come across a planet that’s a History Planet instead of an alien world, in this case, the Old West, and it doesn’t tie to the Xindi arc at all. It’s disposable. For Carpenter Street, it’s having the characters time-travel to modern-day Earth. For that, it does tie to the arc, in that they go back to stop Xindi Reptilians in Earth’s past who are preparing the biological weapon. The time travel is so incidental for both parties, it’s pure handwavium, and raises more “If they can do that…” questions than the arc wants to answer. It does, in the end, provide Capt. Archer with something tangible, and that proves important later… but that could have been achieved without the time travel mess.
Chosen Realm is largely disposable, but it throws a small long-term setback into the mix by having all the data they’ve collected on the Expanse and the spheres deleted from their computer. It’s only small because it doesn’t seem to slow them down significantly. It also introduces the idea of Who Built The Spheres, and that said Builders might be worshiped. Similitude and Doctor’s Orders are also relatively disposable, but both of them are, at least, nice character pieces. Similitude again pushes the character-arc question for Capt. Archer: how far will he go to succeed? In this case, he allows a sentient being to be born and live for a short period of time in order to save Trip’s life, on the principle that he cannot succeed without Trip. The plot requires a lot more of sci-fi handwavium (Dr. Phlox happens to have a Morally Questionable Miracle in the back of his cupboard…), but it works if you can swallow that pill. Doctor’s Orders is fun enough, carried largely by John Billingsley’s charm. It does built off the idea that the Spheres are Changing Space, set up in Harbinger, so that helps give it some purpose.
Fortunately, Proving Ground, Stratagem and Harbinger do some good work. The first two bring the Xindi and the Xindi Weapon into focus, largely through Degra, the Xindi-Primate who is responsible for actually designing the weapon. An excellent job is done in these episodes changing him from a Nameless Councilmember to a real character, someone who has agreed to do something terrible because he believes it’s necessary. Strategem in particular, is a fun exercise, because it plays the “You don’t remember but it’s been a few years and we’re friends now” trope in reverse– having our protagonists be the perpetrators of the trick instead of the victims. But in doing so, Archer gets to know Degra the Man, as opposed to Degra the Weapon Builder, which also helps shift things towards a more Trek-oriented Final Solution. Harbinger, of these three, does suffer somewhat because it feels more disposable than it actually is: it’s mostly character work, filling the time from the travel-with-purpose to Azati Prime (the location of the weapon construction, learned in Strategem) to work on character subplots. It turns the screws on the Trip/T’Pol romance, as well as the Reed/Hayes hostility. And, as mentioned, it sets up the Real Villain: The Sphere Builders. In doing that, the stakes are changed.
However, one should avoid having the word “disposable” being used too much, especially in the middle third of a storyline. It leads your audience to wander away and say, “I don’t know what’s going on, really”. And who wants that? In terms of twelve-part structure, I feel like this only really brings us to Part Five: Payback (with the Sphere Builders being brought into play showing the real stakes). Five/twelfths of story when we’re two-thirds in? Problematic. But it does offer the opportunity for a fast-paced final act.