I wrote something similar on another board (I think? My mind is going.) as Mistress Euclid and Kathy Rose regarding Cogenitor.
I love the Archer/Trip friendship because it's really complex, at least IHMO.
If you're looking at the two as a good friends, my take on this particular friendship when I'm writing is that it had the character of an older/younger brother and mentor/mentee relationship, as opposed to Trip and Malcolm's more college-buddies-like friendship. (Or opposed to Archer's friend-and-competitor type friendships with A.G. Robinson and Shran.)
Because of that, I agree with this wholeheartedly:
Mistress Euclid wrote:Archer saw a little too much of himself in Trip's actions, since Archer had been known to interfere in situations. Consequently, his strongly expressed feelings.
I saw that scene as sort of like when an older brother, who's done some risky behavior (smoking/drugs, something illegal etc. whatever), finds out that his younger sibling who idolizes him has just done something similar thus putting the youth's future at risk. The older sibling comes down far harder on the younger sibling than he would on anyone else out of guilt and an identification with the situation.
It usually has the same effect as it seemed to have with Archer and Trip. There's a bit of a cooling between the two, as the hero worship fades: the younger one begins to view the older a little more realistically and struggles to work out their own way of doing things while the other doesn't want to be idolized anymore and begins to struggle to deal with his own failures. In the best of circumstances this'll pass and the two will reconcile and become close again.
I think the third season was a sort of take on Archer and Trip's personal struggles while the fourth season hinted at the reconciliation and that they'd both grown. If the series had gone on, I could see Archer eventually growing into a wiser diplomat and Federation statesman while mentoring Trip out of engineering and into a leader as a Starfleet Captain and the two remaining friends the rest of their lives.
I also thought Cogenitor was a really nice example of both men's particular virtues catching up with them in a negative way. For Trip, it was his friendliness desire (and ability) to reach out and help those who are a little different. For Archer, it was his positive and optimistic view of exploration and meeting new species. For Trip, his help turned out to have tragic consequences in a situation that was far more complex than it might have seemed on the surface. For Archer, he was maybe shake to realize that he'd been so eager to expereince a positive First Contact that hadn't seen the similarities of this complex social situation to ones in which he'd interfered.
Apologies for the rambling sentences. I think I've had too much caffeine this morning.
