"Marooning a ship full of innocent people?" is a reference to Damage (Episode 3x19)
With a boarding party, Archer, and Trip transport onto the vessel, and
manage to steal their warp coil while leaving behind three containers
of trellium-D as well as other supplies in 'compensation'. When the
Captain asks why Archer is doing this, Archer simply states that he
has no choice before leaving, knowing that by taking their warp coil
the alien crew has been left stranded three years from their home.
"Does that include torture?" is a reference to Anomaly (Episode 3x02)
Archer enters the brig and, holding a phase pistol to Orgoth's neck,
escorts him to the airlock, startling some of the crewmembers on the
way. Shoving him into the airlock, Orgoth refuses to respond, still
thinking Archer is too civilized. Archer starts to decompress the
airlock, saying that if he doesn't talk, he has less than forty
seconds to live...Realizing that Archer wasn't bluffing,
Orgoth says he'll give Archer the information he needs.