The issue is ambiguous in several ways, and the rest of the series may or may not clear up the ambiguity in full. For now, we can wonder about (and likely, debate) some of the facts behind this complex story.
Bruce is simultaneously fighting at least three battles. Most vividly, there is a tentacled maw, a "Lovecraftian horror", that threatens the existence of Gotham City during its earliest days. The strange words Bruce hears after his first battle are Morrison's creation, but use the orthography -- specifically, unusual consonant sequences -- of terms (e.g., Nyarlathotep) that H. P. Lovecraft used in his stories about the Cthulhu Mythos. Bruce's repeated swordplay holds the creature back and eventually smites it.
He also fights against the times, resisting the unreasoned persecution of a Salem-like witch hunt. As the world's greatest detective -- his detective skills are on better display here than we have seen in some time -- he adroitly identifies conventional crime where his foil, Malleus, wants to identify witchcraft and the Devil -- which happen to be present in the story, but not where the witch hunters see them.
Finally, in saving Gotham, Bruce may place his foot into Darkseid's universal death trap; it's possible that he has already by the end of issue #2 escaped it.
The issue opens many possible mysteries, and resolves just a couple of them. Malleus, the overzealous witch hunter, turns out to be Nathaniel Wayne, who is absent from the portraits we have seen in Batman and Robin. Despite Bruce's failure to match the speech patterns of the times, Nathaniel seems not to recognize that Bruce is not the real Mordecai Wayne, so the relation between those two past Waynes is possibly not too close. Nathaniel seems to be earnest in fighting evil, but his ignorance and lack of circumspection does irreparable harm. He kills Bruce's lover, Annie, a real witch but not an evil one. In so doing, he may create the trigger of Darkseid's curse: When Annie curses all Waynes until the end of time, she is unwittingly cursing Bruce, her love. We don't know the consequences, but it may lead to the downfall of both Thomas Waynes. It may even be the thing that weaponizes Bruce and makes him a hazard to the 21st century. This curse echoes the one that Doctor Hurt casts at the end of Batman, R.I.P., and we know that somehow Bruce will beat both curses. Annie, for her part, resembles in some ways the backstory of the fictional Blair Witch, Elly Kedward, as a real witch from the British Isles who lands on the American continent and is soon unjustly exiled to the woods. She also calls to mind both Selina Kyle (the bat-villains suggested on the cover make no overt appearance in the issue) and Zatanna: Her wish for a man brought Bruce to her time, a plot point that Morrison also wrote for Zatanna in Seven Soldiers, when she wished for man who would bring excitement and received an evil destroyer.
The Archivist, who in the issue's biggest surprise turns out to be Bruce himself, reveals a great deal of science fiction that has apparently been part of Morrison's worldview for a long time. Space B was the mechanism by which the aliens who created Animal Man traveled through time, space, and reality, referenced in a Morrison passage in 52 #30. This was also mentioned by Bat-Mite in Batman #673. With remarkable brevity, the Archivist's comments also reinforce the cosmology in Superman Beyond (which Superman recognizes when he hears it; his blue eyes in his last panel may indicate the 4-D vision from that series). He identifies the universe as Universe-Zero, consistent with the Monitors' comments in Final Crisis and possibly relevant to Morrison's upcoming Multiversity miniseries. The notion of the whole universe being written in a single record suggests both the Worlogog from "Rock of Ages" and the book in Superman Beyond. The idea of freezing the whole record and storing it recalls how Superman (in two senses) saved the universe as the end of Final Crisis. The "hyperfauna", which perhaps comprise the real threat in Darkseid's trap, call to mind the higher dimensions of the Chronovore in All Star Superman and the Wonderworld in "Rock of Ages". It is possible that Annie's devils, the "wheel of time" and "neverending world" are the Sheeda from Seven Soldiers. All told, there is a single worldview evident here, and the connections across several Morrison stories surface here more clearly than ever.
Two larger battles stretch across the whole story. While the story of Thomas Wayne's devil worship in 1765 suggested that the Waynes' association with deviltry and demons began then, Return of Bruce Wayne #2 is set significantly earlier, with the portrait artist Brother Martin having studied under Rembrandt van Rijn, who died in 1669. This may downplay the possible importance of old Thomas Wayne in the backstory. Indeed, the story carries back, we now know, to the Miagani "bat people" having been changed from the "deer people" by their contact with Bruce in issue #1. But the first bat in the story is still the giant one killed by Vandal Savage before #1's events. We don't know how far back the bat / devil associations go, but we know from the words of someone who lived after Bruce's adventure in #2 that "the Devil" is not yet done with Gotham. This could refer to 1765's Thomas Wayne or still more plots involving Doctor Hurt. (Nathaniel describes the dragon in #2 with seven heads and ten crowns, terms from the Book of Revelation, chapters 12 and 13.) Meanwhile, the book seen in Mordecai's painting is given an origin here: It was written by Bruce, and thus describes what he knows as of #2, when he is still unclear about the full story. Is the book the artifact that is in the casket in Batman and Robin? Probably not, because, based on the fiends' comments in Batman and Robin #12, it has some apparent power over Barbatos, and there's no reason yet to suspect that a book that Bruce authors at this time would control a demon. More likely, it contains facts that Dick Grayson will soon need to know.
And the other overarching plot: Darkseid's use of Bruce as a weapon to destroy the 21st century? We don't know exactly how that works or how it might be stopped nor how Superman knows that such a trap exists. Annie's curse is one possible explanation. In fact, her curse must have some consequence, and if it is not merely the woes that follow several generations of Wayne, it could be a magical blight on Bruce that will cause the destruction of the universe upon his return. Why do I think so? Deals with the Devil often hang on the fine print. Annie said that the curse would last "until the end of time". So what has Bruce done? We don't know how Bruce became the Archivist. We don't know whether that event comes, in his personal timeline, between issue #2 and #3 or perhaps between #5 and #6. Bruce washes up on a beach to begin his adventure in #3, once again with an eclipse of the Sun at the time of his time jump, clinging to memories from his first two adventures. I think his role as the Archivist comes later in his personal timeline. He will somehow parlay the resources from pirate or cowboy days to travel to Vanishing Point. It looks to me like Bruce Wayne, given a curse that will affect him "until the end of time" went to the end of time in order to escape the curse. The series has four more issues, but we have seen Bruce Wayne already escape one of the problems plaguing him; he has perhaps already checkmated Darkseid.
