* What does Stardraw technology involve, exactly? Is it kind of like solar capture technology, but workable for all types of energy? Even so, it seems more sophisticated than that, since [[spoiler:the Progenitor]] can use it to [[spoiler:''compress the entire universe'']].
* What the heck is a "+ih emitter"? An early prototype of the +ii? What are the differences? Perhaps [[spoiler:that's the only version that's flawed...]]
* Endgame spoilers here: [[spoiler:Is there any real reason why the emitters suddenly fail after an unknown length of time, other than plot contrivance? It just seems kind of out of the blue. If they can preserve cells for billions of years, why not indefinitely? What causes them to fail?]]
* Why do your crewmates have gender exclusion preferences for whether or not they'll fall in love with Ros? You ''could'' say that sexuality is genetic/biological, so they would still have such vestigial traits even if everyone's sterilized...but then why do they have no ''species'' preferences in that case? You'd think that that psychological block would be greater, yet it's apparently nonexistent.
* What exactly are the "colonists" at the end of episode 3? Willis says not to have any moral regrets over killing them, because they're "artificial"? What does that mean? Are they robots? Computer programs? But they must be physical in some capacity, since physical weapons can kill them. And they are ''definitely'' sentient, since [[spoiler:they make the decision to help you in the final mission, something that should be impossibly far outside of their scope if they were programs]].
* Who ''was'' that plant merchant?
** [[http://tilde-one.com/articles.php?id=346 This blog post]] seems to hint that it's [[spoiler:either #1213 or #0EF7, the two biologists from the abandoned databanks. It's clear from the biology room that plant biology was a branch of their abiogenesis projects, and, if they have access to technology on par with the Progenitor, they fit the "means and resources available" clause. We never meet them in person though, so the hints about speech patterns don't fit with this...]]