Throughout every episode released so far, nearly every decision Waver/Lord El-Melloi II makes is animated by his attempt to live up to Iskandar and his sacrifice to protect him from Gilgamesh. He's definitely holding up better than most, but he is definitely hurting (which also colors his relationship with others).
Episode 1: Nearly every attempt Waver makes to do something good after the Fourth Holy Grail War lands him in trouble—with even a simple attempt at fixing someone's bike (who is rushing to buy medicine) through magic leading to him being kidnapped. His positive relief at finding Melvin and saving him (and subsequently convincing Reines of his intentions) is almost cathartic—at leastuntilshe promotes him as Lord El-Melloi against his wishes.
On a Fridge note: It appears that prior to being thrown back into the world of Clock Tower politics, Waver chose to be Walking the Earth and helping people along the way (albeit we really only see him within the countries Iskandar/Alexander formerly conquered). This puts his meeting with Shirou Emiya in the [unlimited blade works] anime in a new light: when he was talking to Shirou about being a "hero of justice" (and cynically commenting about it), he knows exactly what it was like.
Episode 2: The murder mystery reveals that the murdered mage was not even murdered at all—but in fact was trying a botched attempt at immortality and had to be put down. While Gray puts the (now-monstrous) mage down with ease, Waver eventually quizzes his daughter (his former student who asked for his help) why she didn't even try to stop her father even if she most likely knew what he was doing. She simply sadly admits that her inaction (essentially leaving her father to self-destruct) was her only way of freeing herselffrom his controlling environment. Waver immediately understands everything, walking away in melancholy—then we cut to her and her maid, warmly holding hands in relief.
Episode 6 has been mostly-lighthearted—what with Gray, Reines and Luvia in a girls' night out shopping. The very end of the episode kicks us into crisis, however, when it is revealed the relic fragment of Iskandar's cape was stolen—explicitly stated to be done by the people involved in Rail Zeppelin. Waver's interest in this case, understandably, just became It's Personal.
Episode 7 touches on a significant Continuity Snarl within the Fatemultiverse: whether Servants summoned actually remember their previous summoning experiences as collected in the Throne of Heroes. While most viewers (especially those coming from Fate/Grand Order) may assume that this is indeed the case, the original stay night / Zero timeline operates on the assumption that they cannot.note For reference, in the visual novel's Unlimited Blade Works route, Archer sadly notes his experiences in the Fifth War will not bleed into his Counter-Guardian self, meaning the closure his Servant unit got during that war will not affect his bitterness-laden original self. Admittedly, the finale of the 2014 anime adaptation was a bit more ambiguous on this. Saber on the other hand remembered the 4th Holy Grail War by way of loophole as when she was summoned she was still alive as part of the exchange of her joining the Throne after she attained the Grail. This therefore introduces additional drama/tension in Waver's Tragic Dream of seeking to summon Iskandar again—in that despite all his efforts/angst, the Iskandar/Alexander he might potentially meet may not even remember everything they went through after all.
Episode 13 gives two as it wraps up the anime adaptation:
Gray finally gives Waver the present she bought for him in episode 6. Waver asks her to stay by his side in the fight against Dr. Heartless and Faker, which prompts Gray to start crying tears of joy and reply "If you'll have me."
Waver has a dream of Okeanos, the sea at the end of the world that Iskandar sought out in life. As a soft piano arrangement of "You Are My King" plays he sees Iskandar waiting for him in the mist asking Waver to join him. Waver turns it down as he doesn't feel he is ready for it yet and still has to reach the point in his journey that he will be. As the mist begins to clear away Iskandar asks if he's enjoyed that journey so far. Waver breaks down crying in joy when he replies that yes it has, lapsing into his younger voice and calling Iskandar "Rider" once again.
Additional note: in the dream, Iskandar's reaction to finding out Waver has become a teacher is one of mild disbelief, surprise and genuine acceptance. His particular description of Waver, however, as someone who "wring(s) out words in a logical manner" is probably his approximation of Greek philosophers in his time—foremost among them being his own mentor, Aristotle. Iskandar, in effect, is recognizing Waver on the same level as the ancients who taught him—which must be the kind of highest compliment any other mage running on Older Is Better would die for.
Much of this discrimination, as established earlier in Fate/Zero, was promoted by Kayneth's (their teacher's) own supremacist beliefs, which was subsequently hopped on by bullies from established families like Horus, Caimir and Amleth (who were shown to be the ones giving Waver most grief—further driving him to make his choice to jump into the Holy Grail War). Even kinder students like Winner, Melvin and Camus (because of the environment) were unable to do much beyond being individually friendlier to Waver himself.
The extent of Amleth's crime was further revealed in that the feat by which he was promoted to Pride (i.e. the rank of achievement won by Svin through his own effort and El-Melloi II's teaching)—Projection Magic—was facilitated by using Camus's own magic in an experiment Gone Horribly Wrong (ending up with her Magical Circuits damaged beyond repair). While this case would have not gone unaddressed by their teacher—Kayneth—it is established these all happened within the timeframe of Fate/Zero (where he died), making Camus's tragedy an indirect casualty of Waver's involvement, to his horror.
The reunion itself reveals how Waver's bullies became Future Losers for their part (Caimir stuck with a dead-end job, Horus becoming a retained assassin not unlike Kiritsugu). Amleth, despite being publicly the organizer of the reunion (and the "most successful" publicly, was revealed to be in much debt to Melvin and Camus—who were loaning him for his Projection research). Camus, in turn, reveals that she purposely kept him on that financial leash partly as revenge.
To save everyone, El Melloi II/Waver had to break her heart once again, by a) emphasizing to her that despite the Love Epiphany, he can no longer return it for he has already devoted his life to honoring Iskandar's ideal; b) insisting that she finally move on and live in the present; and c) in wrapping up the case, informing her that she can no longer interact with the world of Clock Tower. The one sweet note in this is that in their parting, El Melloi II/Waver finally manages to give her a photo of him with her and Melvin, as well as thanking her for their friendship in their youth. For the first time, Camus leaves with a genuine smile on her face. Later on, as Waver hosts his Christmas movie night with his Family of Choice, a photo of Camus taking a selfie with Waver is prominently displayed near the television.
In the tenth and final volume of the Case Files, Waver finally gets his Big Damn Reunion with Iskandar. It is not the Iskandar he knew, not even the Heroic Spirit but a Divine Spirit from having ascended, and it is pointed out to Waver that he doesn't remember him at all. It doesn't matter: it is still a very emotional moment for him, with him on the verge of tears.
"Sorry, Rider. I wanted your wish to come true. I really wished that your wish would be granted. I really did. You’re always so impatient, always barging into places before you’re ready, making a mess, and then leaving. Shut up and wait for once, will you? Just laugh like you always do and watch me from a distance. I promise I’ll get there one day. You can pat me on the back when I do, you idiot. A promise is a promise, even if no one believes me. I don’t even believe in myself. I know I don’t have the capacity to become a Heroic Spirit. But I will spend my life trying to reach you. Because I am your Master… and your subject… You are my king… And also… my friend…"
It is even more heartbreaking because of how short the reunion has to be, as Waver needs to send Iskandar back to foil the villain's plan.
Heartless' death. After all his machinations and plans and rituals, by the end of it all he has exhausted all his magical reserves and is on the verge of death. Using the last of his powers, he teleports himself and Faker to the outskirts of Albion's Mining City. They reminisce over their pasts and their shared inability to move past nostalgia, Heartless finally accepts to drink wine with Faker, and he finally peacefully expires under the same crystal dome he was born under.
