Fullmetal Alchemist Brotherhood

The brothers find out that there might be information about philosipher stones at the 5th Laboratory, and go to learn, only to meet near deaths and the laboratory being burned down. While there, Alphonse becomes aware that he might not be Ed's actual brother, but just a soul he created of rhis own personal uses, though this is resolved later in the story. The brothers then travel to their friend Winry's residence to get their automail fixed, and before leaving, they burn their former house down, as a representative of "not turning back". The Brothers travel to their old teacher's house to learn more about the Stones, Alphonse is kidnapped by Greed the Hommunculous and rescued, and they Elric brothers learn that their teacher tried transmutating her son, thus losing body organs in the process. After a few episodes, involving fights and the eventual destruction of another Homunculous, Edward learns that what he and Al transmuted wasn't in fact their mother, and both Al and their teacher are relieved that they didn't harm human souls.

The house-burning down happened WELL before most of the events in the plot.

They visited Winry for maintenance after Scar's attack on them; after the 5th Lab, she comes to visit them, since Ed's hospitalized at the time (and she feels guilty over botching the former repair, forgetting a missing screw).

They go to Dublith to see if their teacher knows anything about how they can get their bodies back, and then learn she transmuted her dead baby son. Then Greed gets involved, only to be found out by King Bradley, the homunculus Wrath (though I'm not entirely sure how he learned of the Devil's Nest outside of deus ex machina, but whatever).

Then they meet Ling and his body guards Lan Fan and Fu. They travel back to Central to learn of Maes Hughes' murder, and mope around a while until Maria Ross is convicted, without a trial, of said murder. Ed acts as witness to her "death" at Roy Mustang's hands. The two get split up at Mustang's orders, letting Ed learn that Maria Ross lives; she and Fu leave the plot for a good while. Al winds up involved in Roy's investigation into the homunculi, which culminates in Lust's death and Jean Havoc's paraplegia. Ed meets his father, Van Hohenheim, who in his vast wisdom (even if he hides it behind a somewhat dopey demeanor - one that didn't really carry over to the anime until later on) sparks Ed's investigation into whether human transmutation of dead beings is even possible, which, in the end, proves to be negative - it can't be done. However, since Ed was able to pull Al's soul from the Truth, he suddenly realizes that this mean's Al's body must also still be alive, and thus it must be possible to bring him back.

Hohhenheim's depiction raises a bunch of questions, both in the new opening and in this episode. I suppose I don't mind saying now that before I ever saw either Hohhenheim or Father, I suspected that they were one and the same. When I saw that the Father is depicted more as a "The Dark Lord on his throne" while Hohhenheim appears to be wandering, I decided not to pursue that one theory. However, I didn't rule out all of my suspicions.

The new opening blatantly shows that Hohhenheim looks identical to Father, except perhaps younger. This episode also implies that he is not human, and that he has either a doppelganger or a dark side. (Since this is a dream, I'm thinking the latter) I don't expect the show's going to reveal much more about this any time soon but I do expect it to be important. I am however certain that Hohhenheim is closer to Father than the show had implied in the first two seasons.

Although I expect that Ed and Al are simply allowed to leave because of something like "the plan's not ready and there's nothing they can do to stop it anyway" and Mustang's band is mostly intact except with higher stakes. I don't expect any major characters to die just yet. That said, I think Hawkeye's (I think that's her name) days are numbered and they have been since season 2. Its just a matter of when it would be most dramatic to kill her.

When Gluttony and Alphonse meet Father, Ed, Ling, and Envy return from the Transmutation portal Ed made. Ed and accuses Father of being Hohenheim, which he responds to by saying "Have you mistaken me for someone else?" (in the dub). Father looks over the three (Al, Ed and Ling), then decides that Ling will become the new Greed, which shockingly Ling agrees to (he wants to learn about immortality, and becoming a Homuncoulus provides it for the most part). A big fight then breaks out, with Ed fighting Ling/Greed, Alphonse fighting Envy(?), Scar attempting to fight Father, and May trying to escape from Gluttony. Al tries to help May escape, and ends up hiding her in his armour to protect her, Father lets Ed and Alphonse go (with Envy leading them to Bradley), And Scar stays to finish off the Chimera gatekeepers. Ed and Al take showers (this is where we learn that May is in Al's armour, when he encourages Ed to put his clothes on before she wakes up), then meet up with Fuhrer Bradley, or "Wrath", along with Mustang.

Not at all surprised by the resolution there, but I didn't expect to see Ling be turned into the vessel for Greed. The show made it clear that Ling thinks he can overcome Greed and then take advantage of the power to rule his people and he apparently can jump in from time to time. Meanwhile, the new Greed's character is rather cool, he's got that card-carrying villain aspect of him which I prefer to Envy's obnoxiousness or Gluttony's childlike behavior.

I knew he'd be related to Hohhenheim. There's clearly some very strong connection between the two, for now I probably could simplify it and call them brothers (pretty sure its more complex than that though). I don't know how Truth fits into this but I suspect Father is the god of alchemy whose condescension leads him to do his own dirty work. Hohhenheim seems to have just a little more faith in humans, his relation to Father would probably make his children something like the chosen ones which would fit all the requisite tropes for an overarching story with a supernatural villain.

Alkahestry probably has its own god, which isn't Hohhenheim because he's already associated with Alchemy and he seemed to notice the effect when Father withdrew the power of Alchemy from Amestris for a short period of time. He's probably the Ishvalan god, and they are probably both related to Truth. While Truth remains withdrawn, these demigods get involved in this conflict. We haven't seen much about Alkahestry so I'm not sure what guesses to make about that god except that at one point in time, the god of alchemy and of alkahestry must have been united based on the evidence from that one city that I can't remember the name of.

Father uses a copy of Hohenheim's body. They are in no way related besides that.

Actually, Father/Dwarf-in-the-Flask "Homunculus" was borne of Hohenheim's blood, so they're technically very related.

As long as I'm in a spoiler box, reading about JEV's absolute certainty that Hawkeye dies leaves me tempted to give him this screenshot from episode 58 entirely out-of-context. :P

Technically yes, but just because that blood was used doesn't necessarily mean they're related. In terms of having similar blood yes, but other than that there is no connection. If Father was an actual human, and not just a Human-esque being using Hohenheim's body and blood, it would be different, but in a way, they aren't related.

Basically what I'm saying is that they can or can't be related, based on how you think about the subject.