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The events of Heroes in Crisis will be undone by Doomsday Clock
Since everything in the comic is leading to the ticking of the In-Universe Doomsday Clock towards midnight.

It’s Poison Ivy.
Booster and Harley both claim to have seen each other commit the murders. One possible answer to this is that both were mind-controlled into doing it.

We further know that Ivy is at sanctuary (as per “Everybody Loves Ivy” from Batman (Tom King)) and has mind-control abilities. She also has the best chance of anyone of getting closer to Harley (though that leaves out how she got control of Booster).

She also had a bit of a breakdown in “Everybody Loves Ivy,” which could be used as an explanation for her murderous actions.

Harley is lying when she says she thinks Booster Gold did it. She actually thinks (wrongly) that Poison Ivy is the murderer.
Harley had temporary access to Wonder Woman's lasso of truth during the scene where she is trying to convince the Trinity that Booster is guilty. However, she notably never says he is the murderer while she is holding the lasso, despite that fact that this would make her claim much more credible. Why would she avoid using this to her advantage to attempt to convince the Trinity of the truth?

In addition, Harley later has a scene where she appears to mourn Ivy, where she says there are many things she regrets and says she should never have helped Ivy or the Joker. She is drawing this analogy, because, out of her desire to help Ivy, she is currently trying to frame someone else to save her. This parallels her relationship with the Joker, where she did awful things for her "puddin'" in the name of love (and is probably why she has returned to her old costume — it is symbolic of slipping back into the old Harley Quinn who is trapped doing terrible things in a horrible relationship).

Possible series of events:

  • Ivy through her own free will or, more likely, because she was forced to by the mysterious Puddlers, takes over one or several of the heroes at Sanctuary, forcing them to attack the others. Some people, including Harley and Booster Gold, are not controlled for whatever reason.

  • Harley realizes it is Ivy's work and in self defense kills some of the heroes who attack her (likely including Commander Steel, based on his autopsy).

  • Booster Gold arrives during the chaos and sees Harley doing the killing. He's not the most stable right now, so he incorrectly concludes that SHE is the killer and flees.

  • Harley has a breakdown because she knows that Ivy could possibly be locked away for life, executed, or murdered in revenge for the killings, and she can't handle that.

  • Harley decides to frame Booster Gold because as a psychologist she knows he is not exactly mentally stable right now and has a guilt complex about his previous time meddling adventures. Booster thus can be easily convinced that he lost his mind and committed the murders unawares.

Wally accidentally or intentionally caused an error that allowed the simulations to escape the room.

When Wally sees Roy's dead body, he asks "why did it...?", followed by the statement "the kids...I didn't want to be alone." Why would he react with precisely these words?

It's possible he, intentionally or unintentionally, caused a system error that allowed things from the Simulation Rooms to interact with the real world. His words may be an expression of guilt at the realization that this has caused immeasurable damage. Essentially, he may be asking "Why did the computer do this?" and trying brokenly to admit to the (dead) Roy that he did it. [This could also potentially explain Harley attacking him.]

The Booster Gold we are seeing is NOT the real Booster Gold.
In his simulation, Booster Gold creates a copy of himself to talk to. When the alarms go off, the simulation remains, despite the fact that the computer apparently wants everyone to evacuate. Why would the computer allow the simulation to persist? After all, the simulations could potentially distract people from evacuating. Jumping off the previous theory, the simulations have somehow escaped into the real world and this Booster Gold is one of them.

[As a bonus, this would mean that when this Booster Gold says "it's my first day" in reply to Harley, he is speaking literally. It's the first day the copy has been alive.]

Supporting evidence:

  • Booster doubts his own memory
  • Booster is "not sure" whether he killed people. He doubts himself because he is Sanctuary, who did kill people.
  • Booster's actual shields work perfectly, but Sanctuary cannot simulate them, which is why they "failed."
  • Booster has been out of character during most of his interactions with characters.

There are two sets of antagonists: "The Puddlers" and "the Puddler killers," who have different goals.
In issue 1, a sign saying "The Puddlers are all dead" appears above the destroyed Sanctuary robots. In issue 2, a mysterious video is sent to Lois Lane written by "The Puddlers."

Two options seem possible to explain the apparent conflict:

1) The Puddler Killer was unhappy with Sanctuary's efforts and decided to Klingon promote him/herself into the new Puddler — by killing all "flawed" heroes.

2) The Puddler Killer and The Puddlers are in fact different. One set, the Puddlers, (misguidedly) wants to "help" by releasing the Heroes' secrets to the world. The other set, the "Killers," attempted to destroy Sanctuary to stop this from occurring.

One of the bodies is Nemesis, not whoever it appears to be
Nemesis's entire schtick is that halfway through a Suicide Squad arc someone would take off a mask and reveal themselves to be him. It's likely that a similar twist is planned here, as he was among the heroes at Sanctuary but his body was not seen. Roy seems the most likely, as he's a B-lister who's generally popular, so a fake-out death is more likely than any of the C-Listers. Perhaps Nemesis intentionally sacrificed himself to save him, or there might be another reason why he'd disguise himself as Roy.
  • Other possibilities include that Nemesis is playing someone alive such as Booster Gold or even Harley Quinn.
  • Wally West seems an unlikely candidate, since we saw him using superspeed immediately before his death (although they could have swapped invisibly using superspeed).
  • One problem with the Roy theory is that Roy's body was already buried, meaning that, if true, the disguise was either good enough to escape autopsy or an autopsy was not performed.

Hi C is an allegory for how DC Editorial prioritizes big sellers like Quinn over legacies

  • Harley is unusually overpowered, while Booster Gold is underpowered. This is played up by Harley casually escaping the Trinity.
  • Several legacies were killed, and this is highlighted in issue four with the Titans mural. The issue itself is titled "$@%!@ this!"
  • Some have theorized that the comic itself is a metacommentary on DC's uncertainty about what they should do with legacy characters. Under this theory, Sanctuary is a stand in for DC editorial, constantly trying the same failed tactics ("treatments") to fix legacies they don't know what to do with, only to result in reliving the trauma and making things worse.

Donna's confession hints that Sanctuary is not a real place

Donna's confession appears to be merely a jab at DC's inability to keep her backstory coherent, but she spends a lot of time talking about the city of Troy and whether it actually existed. This could be a hint that the entirety of Sanctuary is in fact a simulation and nothing we see is real. This would explain some oddities, like some bodies shifting positions between comics and the confusing layout (the place seems fairly small, yet apparently housed several dozen heroes). It's possible the entire world of "Sanctuary" is a simulation everyone is trapped in.

Wally is being framed by Zoom

The very existence of a place like Sanctuary runs directly counter to Hunter Zolomon's philosophy that tragedy makes heroes stronger, and the reveal of issue #7's cover has Poison Ivy drawing what could be Zoom's chest symbol from the dead character's perspective. Zoom's background as a profiler and time travel abilities could explain much of the plot twists.

The biggest flaw in this reasoning is, of course, that as of #5 Zoom's not even been referenced.

  • Disproven in #8.
  • Flash 761 reveals that Eobard Thawne was using the Speedforce to manipulate Wally's actions. Close enough.

The original story intended by Tom King for this series was drastically different

  • Wally was probably always meant to be the culprit, at least once Tom King was given the characters he would use by editorial based on the plot outline he turned in, but I'm guessing that the original story placed a lot more blame on the Trinity for Sanctuary's failure (and admitted Sancuarty WAS a failure), and also made a lot more sense than the story we got, but editorial vetoed it. They were fine with Wally being the killer, but the idea of the Trinity being implicated and held partly responsible for a massacre of heroes was too much for editorial to accept. This meant that the plot thread involving the Sanctuary AI had be dropped completely because it's already been established to have been made by the Trinity of their supposed best aspects, and even acknowledging Sanctuary's issues wasn't allowed since the Trinity would be held responsible for that. But none of the implications were removed, they just went unaddressed. Also, maybe, in the original scenario, Wally wasn't going to be the one that reassembled the video files, rather the AI would have reassembled them, never have deleted them in the first place, or made copies of each confession before deleting the original, then at some point would've manipulated Wally into watching them, with Wally suffering a very similar reaction as in the series we got. It's also possible that, under this plan, the massacre wouldn't have been some accident involving a hitherto unmentioned power of the Speed Force. Wally would've actually killed all the other people at Sanctuary, but because editorial vetoed implicating the Trinity and sharing some of the blame, that would've meant Wally would've been held solely responsible and blamed for murdering the other heroes, without the AI manipulating him to do it, something Tom King thought was too much, so he rewrote it to be an accident, but since it was an accident, he then needed to come up with some way to still have a murder mystery, so Wally's crime became... everything we saw in the series. There is absolutely nothing to indicate that this was the original plan, but it seems pretty clear that the final story we got was altered heavily at some point for some reason. Also, my logic is that editorial only vetoed King's original AFTER the series began being published, and thus he had to work within the existing framework already established and needed more issues to buy time to come up with another resolution, hence the issues that focus exclusively on Sanctuary before the massacre. It's worth pointing out that a lot of the aspects of the ending of the series and the explanation for the crime were only introduced late in the series. Speed Force explosion and Wally's sudden mastery of computers are rather inexplicable and never hinted at all in the series itself until the issue that it's all revealed. The series occurring over the span of only five days is only introduced, I believe, in the penultimate issue, but perhaps that wasn't always the intention, hence why The Price, which was published quite a while before Issue #8 contradicts it, despite that being a pretty significant detail to not share if it was already decided and was so prominent. Also, Booster Gold's solution to the problem of Wally's dead body using cloning comes out of nowhere, despite the fact it wouldn't have been that hard to foreshadow beforehand... unless maybe the original plan was that Wally wasn't going to survive, hence they didn't set up a way to get out of it beforehand, this would also explain why The Flash Annual tie-in was written like the character was dead, because when Williamson wrote it, its possible he thought the character would be dead ultimately. Whether he lived because editorial caught the fan backlash to the series or Tom King decided there was no point given everything else being altered, they needed a way to explain the dead body so they pulled one out of thin air that, while not set up beforehand, isn't total nonsense.
  • This probably sounds more like I'm trying to absolve King and blame editorial, which I'm not. I probably wouldn't have liked this story much either, but this was the most logical solution I could come up with for what may have happened given the info available. I feel it makes a bit more sense than what we got, but also is quite a bit bleaker (but given this is King, that could only make it more likely).

The whole story was part of Zoom's Misery Builds Character gambit

While an earlier post above proposed that Wally was being framed by Zoom, this one proposes that the whole concept of Sanctuary was one big plan by Hunter Zolomon to, once again, attempt to force his belief that "tragedy makes better heroes" onto Wally. Sanctuary as a place for superheroes to seek counselling for PTSD would be completely in line with Zoom's M.O. (he was previously a criminal psychologist who worked as an FBI profiler), and he had previously manipulated Wally into fighting with Barry by using the prospect of restoring Wally's family as bait.

Abra Kadabra was the Man Behind the Man

Abra Kadabra has had experience with psychologically tormenting Wally through his removal of Linda from the timeline so that nobody (except Bart Allen) would remember she ever existed. He's also had experience manipulating events to bring a Flash character into public disgrace. Since the failure of those previous plans, Kadabra has had time to refine his tactics, adapting the first one to include Wally's kids along with Linda, and bringing the second one to fruition by getting Wally in trouble with the law as a murderer.

  • For bonus points, in conjunction with the WMG immediately above, Kadabra could be working with Hunter Zolomon to make Wally even more miserable.

The series was strictly meant to be a murder mystery a la Identity Crisis. Nothing more and nothing deeper than that.

Sanctuary is simply a means to get a bunch of heroes in one place for a shock-and-kill plotline. Others have dissected the nonsensical approach to mental health and trauma. The series wasn't meant to make any larger point about these subjects. It had an Eisner Award-winning writer and a fan-favorite character (who wasn't so well-loved by the company's management), so DC probably figured these factors and a murder mystery plot (shades of Identity Crisis) would goose sales. The series was never marketed as any sort of deep exploration of mental health. Promotions emphasized the murder mystery theme and character deaths. It explains the holes in the plotline where therapy and mental health are concerned. The people involved simply weren't interested in that. They intended to do another Identity Crisis.

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