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What did Charlotte Keene's F-35 squadron run into before crashing in Silo season 3 episode 1?

In Silo episode 301, Charlotte Keene's Navy squadron encounters something disturbing at altitude.
Silo season 3. Photo Courtesy of Apple.
Silo season 3. Photo Courtesy of Apple.

Season 3 episode 1 of Silo dropped one of its most unsettling scenes yet that showed a Navy F-35 cockpit filling with a thick, oily substance that moves like it has a mind of its own moments before the jet goes down. If you blinked, rewound, and still aren't sure what you just watched, you're in good company. Here's a full breakdown of the sequence and what we currently think it is.

The 'before times' storyline of the episode opens with a scene that plays like something out of a Cold War thriller. A woman moves through Washington DC, changing her appearance mid-journey and switching subway trains because she suspects someone is following her. That woman turns out to be Charlotte Keene, or Charles as her brother calls her, played by Jessica Brown Findlay.

She eventually meets up with her brother, Congressman Daniel Keene (Ashley Zukerman) whom we saw in the season 2 finale, and immediately checks whether he followed her counter-surveillance instructions before letting the conversation go anywhere. The siblings bicker a little and there's this easy, lived-in chemistry between them. But the point of the meeting seems quite serious. Charlotte wants Daniel to use his position to get onto Senator Rosalind Thurman's Iran committee. What she doesn't tell him is what her own assignment is, despite being asked.

Silo season 3. Photo Courtesy of Apple.
Silo season 3. Photo Courtesy of Apple.

Charlotte Keene was on a 'double tap' mission

Shortly after, we learn what Charlotte is actually doing when Daniel approaches Thruman asking to be placed on the committee so he knows about his sister's whereabouts and involvement at the Nimitz. She's a Navy aviator, and Daniel is later informed that she and her squadron are flying F-35s from the USS Nimitz on a retaliatory strike mission against Iran. We learned in the season 2 finale that the U.S. has been hit with what the government is calling an Iranian dirty bomb, and this flight is apparently the response.

The squadron climbs to 50,000 feet for what appears to be a coordinated strike alongside missiles already launched from the Nimitz. The plan is a 'double tap' where the ship's missiles go first and Charlotte and her team's jets follow up to make sure a certain 'mountain facility target' is destroyed. Standard enough for a military thriller and nothing about it feels supernatural yet.

Then they hit a mysterious cloud that appears at altitude and doesn't behave like any atmospheric phenomenon the pilots recognize, and they comment it has no business being where it is at 50,000 feet.

As the jets fly into it, things start going wrong almost immediately. The aircrafts begin to malfunction and formation breaks apart. But the really disturbing part is what happens when the wreckage from the disintegrating jets appears to melt, merge and recombine in a way that is uncanny to watch.

Inside the cockpit, Charlotte encounters the substance directly. It enters the aircraft, or perhaps it was already there, and it coats the control panel. Other pilots confirm the same. There's a shot of Charlotte pulling her hand away from a surface and watching thin tendrils of liquidish stuff stretch between her fingers before snapping.

The squadron is destroyed. Charlotte survives and is eventually found near Turkmenistan, per Thruman who informs Daniel. When Daniel rushes to reach her, he's told she's been redirected from Walter Reed to the Heidi Stensen Clinic in Fairfax, a specialist neurological facility and apparently the go-to place for traumatic brain injury. When he finally gets to her, she's alive but bruised, and she has no idea who he is.

SPOILERS ahead for Hugh Howey's source novels Shift and Dust.

So what is the liquid-ish substance in Silo?

The show doesn't tell us just yet about this in episode 1. The leading theory, and the one the show is almost certainly building toward from the books, is that Charlotte's squadron flew into a cloud of self-replicating nanobots. Those are microscopic machines, small enough to be invisible individually and capable of breaking down and rebuilding matter at a molecular level. The 'melting' wreckage of the flight scene is apparently depicting the aircraft being disassembled and repurposed by something operating below the threshold of the naked eye. The black liquid-ish thing is what a nanobot swarm dense enough to be visible looks like.

Whether the cloud was an Iranian weapon, a U.S. experiment gone wrong or something else entirely is the question the season will presumably answer in the next episodes. Now let's go even deeper into MAJOR SPOILERS from Shift and Dust.

What the books tell us (And what the show is inventing here)

Now, Charlotte Keene's F-35 mission and the crash doesn't particularly exist in Hugh Howey's books. In Shift, Charlotte Keene is indeed described as a veteran drone pilot struggling to adjust to civilian life after service in Iraq, but her main function in the book's pre-silo timeline sees her helping Donald (the book's version of Daniel) by getting a prescription filed under her name, which later turns out to be the reason he has partial immunity to the memory-suppression drugs. That's essentially it for her pre-silo story.

Silo season 3. Photo Courtesy of Apple.
Silo season 3. Photo Courtesy of Apple.

The Iran angle does exist in the books, but only as retroactive justification. In the novels, Thurman explains well after the apocalypse has already happened, that Iranian actors weaponized nanotech. Thurman's response was orchestrating a nuclear reset of civilization, with the silos already built as the ark, as the preemptive answer to a nanoterrorism threat he (in the books it's Paul Thurman by the way) believed was inevitable.

What the show is doing is dramatizing all of that backstory. It's so far built a thriller-paced origin story around it and I'm absolutely loving it.

Also, the books do eventually confirm that the toxic 'dust' surrounding the silos is itself a nanobot cloud keeping the residents from perceiving the truth about the outside world, so the visual logic connects.

We'll learn more as new episodes of Silo season 3 drop Fridays on Apple TV.

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