The resolution of Chac's sidequest, in which Sorenson himself helps pull Chac back from the Despair Event Horizon.
At the resolution of Soran's sidequest, if you are inquisitive enough, you can learn what he's using all that carboderm for. He wants to seal himself in a ball of the stuff until society's rebuilt and everything returns to normal -- he doesn't care how long. Effectively, it's suicide. If you are persuasive enough, you can talk him out of it and convince him he has a purpose in life.
All of your crewmates banding together and defending you from Thomas' verbal assaults in episode 4, each of them creating an on-the-spot Rousing Speech.
Crowning Music of Awesome: Space Lizard is making a completely unique soundtrack this time around, and some themes are pretty catchy. Of note:
Also Hunting, the BGM for bounty hunt missions. The perky, laid-back, upbeat music contrasted with the heavy, serious riffs from Engorging makes for a very interesting effect.
And Enclosing, the BGM for the final mission. It captures the tension and drama of a final dungeon well.
Fridge Horror: Failing to capture the orbital containment sphere before it falls into the atmosphere and disintegrates would mean that Daszk dies a horrible death, as he's trapped there with no way to get out...
"All Good Things" is a reference to the proverb "all good things must come to pass", which probably refers to the Backstory of the Shine destroying almost all of humanity's accomplishments.
"Castles of Sand" is also a reference to a proverb, with the meaning of a fortress that seems secure, but is actually worthless and easily infiltrated/destroyed. Since episode 1 revolves around defending and rebuilding, that's pretty ominous.
"His Master's Voice" was the slogan of a recording company, who claimed that their recording technology was so authentic that a dog would not be able to differentiate between the record and its master ... and in The Reconstruction, we have a group of "Watchers" who claim to take orders from "The Voice Himself". Possible Foreshadowing?
Typelog also records information, so it could be referencing that.
"And Yet It Moves" are the words that Galileo (supposedly) muttered under his breath at his trial after being forced to recant the Copernican theory. Episode 3 revolves around EROS, a secretive group whose views clash with those of Typelog. Most likely, the famous phrase is meant to draw a parallel to their conflict with Typelog -- conforming to the unquestionable views of authority versus freedom and a lack of limitations on science.
"Forever And Ever" is a common phrase in The Bible, usually referring to God or the heavens. Though we can't be certain of its significance yet, it seems to be be an ironic counterpoise to a major theme introduced in episode 4, which is that nothing lasts forever or is truly infinite.
"A Plan For Everything" is also a religious reference -- God is often said to have planned out the destinies of all aspects of the world in advance. Only time will tell the full meaning behind this reference.
Needs More Love: Curiously, it actually seems to be getting more publicity than The Reconstruction, despite the necessity to play the first game to understand the plot and avoid massive spoilers. Only marginally more publicity, though; the game still Needs More Love.
That One Attack: Pretty much every boss' attack, though particularly Irradiation Field and Punishment Sphere, used by the twins. They have a base attack power of 900 permille. If it's any consolation, you're pretty much guaranteed to get the merit for dying in one hit - if you didn't already get it already with Tezkhra from the Black One.
What an Idiot!: Both characteristically and uncharacteristically for Tezkhra, he admits in one side conversation that he deletes his Typelog files if he doesn't think they're necessary, to maintain order and conserve space. How he didn't think this would come back to bite him is beyond us. Probably it's an excuse he made up himself though, and the real reason was crucial information about his identity no one should know about, including himself.