It's not surprising or unusual to become confused in this chapter as the author is dealing with some weighty material, that is, quantum physics. Very briefly, quantum physics is the study of the atomic activity of particulate matter.
In this chapter, Charles Wallace and the unicorn Gaudior are attempting something Guadior finds nearly impossible, to travel not only back in time, "When", but also in space, "Where." Also complicating matters is the pursuit of the Echthroi, (in Greek, this literally translates to "the enemy," an apt name L'Engle gives to race of beings who are trying to destroy the universe by "un-Naming" things.) Guadior defines these alternate spaces as "elsewhen" and "elsewhere."
Charles Wallace wants to go back to the year 1865. He wants to find out why a group of Welshmen are traveling to South America, the place where Matthew Maddox published his first novel, about the legend of Maddoc Gwenydd. Reluctantly, Gaudior agrees to try.
They do not get far. Almost immediately, the Echthroi attack, bringing with them their "horrible stench." Gaudior battles the evil beings and overcomes them, just barely able to save Charles Wallace, who has lost his grip on the mane and fallen. He carries the boy in his mouth. Eventually, the land safely on the star-watching rock.
Charles is immediately concerned that they have not arrived at the right "When." He explains to Gaudior that this is imperative if there is a "Might-Have-Been" that they are supposed to discover. Gaudior chastises the boy and tells him he needs to concentrate on being "Within," that is, to get out of his own body and into another spiritual dimension (again, particulate theory, quantum physics). Gaudior wraps Charles Wallace in his wing; struggle is useless. When he awakens, he is "within," and within Brandon Llawcae, a "seer" in a village of settlers in the New World.
In this body, Charles Wallace is younger than his real self, perhaps eleven or twelve. He is approached by a woman, whom he calls out to, shouting, "Zylle!" Zylle speaks about someone else, calling her friend "Goody." Charles knows that this title, short for "goodwife," is a term used by the Pilgrims. It is the wrong "When." Pilgrims date almost two hundred years prior to 1865.
Charles is irritated but Gaudior urges him to be patient, to stay, and to "be Brandon."
Charles Wallace decides to take this advice and stick around. Zylle, whom he had met while she was picking medicinal herbs, shortly after becoming Charles-Wallace-within-Brandon, is pregnant. He is there for the birth of her baby. He learns from her and from the body and brain that he now inhabits, that he is a "seer." As such, he "sees" a picture of the child yet-to-be-born. It is a boy.
This child, whom Zylle and her husband Ritchie, name "Bran" after Brandon, will be the "Might-Have-Been" Charles Wallace was hoping for and the clue they would have missed had they not gone so far back "elsewhen."