Parts one, two and three.
The third act of the Xindi Arc is pretty action packed. On some level, it does make up for the heel-dragging and aimlessness of the first two thirds: Episodes are: "Hatchery", "Azati Prime", "Damage", "The Forgotten", "E2", "The Council", "Countdown" and "Zero Hour".
Of these eight, really only two are inessential: "Hatchery" and "E2". But both of them do speak to the character of the Enterprise crew. Since the one character-arc that's really tied to story-arc is "How far will Archer go?", to a degree "Hatchery" answers the question, "How far will the crew let him go?" Now, it approaches it from a different angle, where Archer goes to extreme measures to help a creche of Xindi-Insectoid infants, and the crew, sensing something wrong, engage in a mini-mutiny. As Archer is Being Affected By Something (a Trek staple to avoid actual conflict or responsibility), the real conflict boils down to the crew vs. Major Hayes, since Hayes just follows orders. This is also the closest thing we get to something resembling focus on the Xindi-Insectoids, who in terms of story never amount to actual characters, simply additional muscle to back up the Reptilians. "E2" is a kind of fun what-might-be time-travel episode, where the crew meets their descendents from a failed future-version of their mission, but other than turning the screws a bit tighter on the Trip/T'Pol romance, it's largely a placeholder.
That said, the three in between those episodes, "Azati Prime", "Damage" and "The Forgotten" do a very nice job illustrating the Collapse-Retreat-Recovery aspect of the Twelve-Part structure. The ship is really hammered, but at the same time Archer makes some connection with Degra and the other Xindi-Primates. It's here that the core Trek principles are pushed to their limits: having discovered the Xindi world-destroyer weapon, the first plan is just to blow it up. This goes wrong, and Archer gets captured, but in being captured, he uses his knowledge from "Stratagem" to his advantage. This convinces Degra enough to at least listen, and stop the Reptilians from attacking the Enterprise. Degra (with the help of the semi-enigmatic Aquatics) returns Archer to the broken ship, and sends message for a secret rendezvous a few light-years away. The ship being in such a state, making that rendezvous is impossible without a new warp-coil. Fortunately, there's another damaged ship nearby, and Archer feels forced to take theirs by force in order to make the meeting. This is without question his lowest point, committing for all intents an act of piracy in the name of saving Earth. It's very non-Trek, which works excellently for the sake of drama. Capt. Archer is torn up to do it, but he feels he has no choice. You could easily see, for example, Cmdr. Adama, John Crichton or Malcolm Reynolds doing the exact same thing under the same circumstances. The only question is, would they feel the same weight? As horrible as the act is, it is in service of, ultimately, a Trek-solution: solving the Xindi situation through dialogue instead of violence.
Of course, the cracks in the plotting armor are quite evident. Degra could have this clandestine meeting somewhere easier for Archer to reach, given that Degra knows the state Enterprise is in. He even could just go to Enterprise directly, and not even be clandestine. The need for secrecy from the Reptilians (and Insectoids) is a bit artificial. And that's a big part of the problem with this plotting, in that it forces Enterprise to go from Point A to Point B (this necessitating the stolen warp coil) and then from Point B to Point C (this using the subspace passage that creates the timetravel accident in E2, which is neatly avoided, meaning the second Enterprise may have "never existed".) It's mostly hoop-jumping so Degra can use Archer as a surprise in "The Council".
"The Council" is, in theory, Archer presenting his case that Earth is not a danger to the Xindi and that the Sphere-Builders/Guardians have been playing the Xindi for their own purposes. It's the latter point that is most crucial, since the Guardians are worshiped as deities by the Xindi, though they were unaware of the connection between the Guardians and the Spheres. While the Xindi Council has five groups, really only three matter: the Arboreals back up the Primates, and the Insectoids back up the Reptilians. And the Aquatics are the enigmatic deciders. In terms of character, it really boils down to Degra (Primate) and Dolim (Reptilian).
It should be noted that Randy Oglesby and Scott MacDonald deserve a lot of praise. Both are journeyman actors who have done tons of guest roles on various shows, including all four of the modern Treks.* They do solid work, often under a lot of latex, and you have to respect that kind of actor. In fact the real dramatic centerpiece of "The Council", and to a degree the turning point of the story arc itself, is between these two actors.
The final wrap-up of "Countdown" and "Zero Hour" is serviceable, in that the Xindi-Reptilians cement their role as the irredeemable villains, who have tied themselves to the Guardians. The Guardians, of course, want to reshape reality-- terraforming our space, as it were, to one that they can survive in. The Reptilians are their willing dupes. Even the Insectoids wise-up, though all they do is wonder why the Spheres are suddenly working to help their efforts to destroy the Earth before the Reptilians sudden-but-inevitable betrayal. The final push, in which Archer enlists Reed and Hoshi to destroy the weapon, saving the Earth, while Trip, T'Pol and Phlox destroy the Spheres themselves, saving the Xindi (and all of reality)-- is entertaining and fun, but sadly mostly involves pushing buttons and punching aliens. The highlight in terms of What-Makes-It-Trek is not the bit where annoying-time-travel-exposition-fairy Daniels pulls Archer to the founding of the Federation (to convince Archer not to sacrifice himself, something Archer is pretty hellbent to do). Instead, it's the moment where the Andorians show up to help defend the Earth. Jeffery Combs-- another strong member of Trek character-actor stable-- sells the hell out of it as the Andorian Commander Shran, and that's a lot of fun.
But in the end, it's a Big Finale: Things go Boom, and the Day Is Saved? Is that all there is? Is that all there can be? That's the big question remaining.
*- I'm fairly certain that the two of them and Jonathan Frakes are the only actors to appear in all four modern Treks.