So this patch is about setting up and exploring two different characters, both independently and in comparison: Real Sphene, and Calyx. It does pretty well with both of these, honestly!
Real Sphene's whole journey is in grappling with what relationship she has in this world she's woken up in, and to a lesser degree her relationship with the Endless Sphene. We see her go from 'I should not be the ruler of a country that's moved on without me', to 'whoever should be ruler it's definitely not these guys', to 'if somebody needs to take the throne, I'll do it'. It works, and I approve, but it's one that's only really nailed down by both her relationship to Calyx (I'll get to him), and Endless Sphene. I like the angle they take, where Real Sphene genuinely doesn't seem to approve of Endless Sphene's actions, and reflexively wants to believe she'd do differently... but at the same time, recognizes Endless Sphene herself as evidence that this is exactly what she'd do. It's an interesting union of the reactions Emet and Venat had to hearing about the End of Days; she has Emet's denial, but it gives way to Venat's recognition that, yes, she would do this.
I also like the minor detail that, unlike Endless Sphene, Real Sphene never uses the name 'Lamat'yi'; it's always 'Wuk Lamat'. I think it shows that Real Sphene actually wants to keep more of a distance; Endless Sphene immediately picked up 'Lamat'yi' and started using it to ingratiate herself as a trustworthy friend, but Real Sphene doesn't know her place in the world, and doesn't want to presume or force one.
And Calyx I immediately love as an antagonist; he's our Kuja, motivated by the desire to escape death, but rooted not so much in fear like Kuja, and more of a broken, hyper-logical altriusm: "I have a solution, and above all else, I will achieve it." It's kind of great that his plan is... honestly a lateral move from Endless Sphene's morality-wise; it's just as bad, and just as dangerous, but in slightly different ways... but the details and precision are what makes Calyx scarier, because it means he's thought about it. He'll melt down all of reality for fuel to save five thousand people, because he's run the numbers and five thousand is sustainable. Just the notion that someone would do those calculations is horrifying, and it means he's turned up with a way more concrete plan than anyone we've faced before.
As for lore hooks: we now have Dali confirmed as another location on the Ninth, as well as confirmation that people have earnestly speculated on: that yes, porxies can cure levin sickness (and it just took a very high-priority patient for Alisaie to give it a shot), but that the environment of Alexandria that caused it will still threaten a relapse. Incidentally, it's bitterly ironic that we discover this in the same patch as we meet Calyx, who was initially motivated by it, but at this point he's too far gone for it to even be worth saying. There's also the very clear and deliberate hook that Calyx calls our world and his 'the Source' and 'the Ninth'; even Krile calls that out as weird, that's clearly adopted language. As it happens, the first person to use numbered designators for shards was Ardbert (naming both the First and Thirteenth in the same cutscene), who definitely learned it from the Ascians... but if Calyx was the same, he would have learned it a very long time ago. I'm even doubtful of that; given the history of the key, it's entirely possible he learned it a few degrees removed from that source.
The tube in Calyx's neck. As it happens I have some personal experience with stuff like this, and would've called it a nerdy tangent... if Calyx hadn't specifically reached out to touch it in that final cutscene. So, here's some detail on what that might be if we presume accurate medical reference.
That's definitely a tube to contain some sort of fluid; there's a port around his chest, and you'd do that 'loop' inside the bandage for fluid but not, say, a wire. In the neck, that's more likely to be an 'in' rather than an 'out' tube, that isn't where you'd put an IV; more likely that's a drain, to either get excess fluid out of the body, or to circumvent the body's circulation in the event the body can't do the whole thing. The bandage suggests that it's either a short-term solution, or that Calyx was moving very little; there's more permanent solutions for people who have to deal with this long-term.
Chances are, this was what Calyx looked like when he died ...and that he was probably doing quite poorly in hospital when he did.