For me, the theme of Season Three has always been about how you have to hit your lowest point before you can reach your highest. That's exactly what Archer goes through here. He starts off all eager and happy-go-lucky in the first season, but as the first season goes on (and especially into the second season) you can clearly tell that Archer is growing more cautious, even a little jaded. Then Earth is attacked in "The Expanse" and that's pretty much it for Archer the Boy Scout. He's decided that the galaxy isn't interested in being friends, so he's going to stop trying.
Then when Season Four comes around (particularly after "Home") Archer starts to pull back away from that darkness and starts to grow into the great captain and leader that Daniels kept going on about. It's actually one of the most interesting character arcs in all of Trek, IMO.