I like the Lucian Alliance Takes over Destiny thread (1.18 - 1.20).
Rush was great as a Spy, and it's always nice seeing him get knocked around
It's nice to Mike Dopud join the show and also nice to have Robert Kneffer around for a few episodes. Eli's cute redhead is the girl that shot the guy that took over for Kiva, right? She's a nice addition too.
Lots of little side stories that were entertaining Scott outside the ship and Eli and Chloe's quest.
And in 2.1 Intervention, poor TJ. The ship may have seen it as helping her cope, but, I'm not sure that was any better than facing the truth, and it helps her down her character slide, IMHO. I do like her relationship with the Mike Dopud character though, they work well together