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    Holographic puzzles 
  • These weird holographic... puzzles?... that Alyx has to get past to access Combine machinery. What is their purpose? Are they meant to be like a lock and key system? If so, the fact that we can reverse engineer the key within seconds shows just how crappy a lock they are, and that a simply password (or even an actual padlock) would've been a more effective alternative. Are they simple On buttons? If so, they're needlessly overcomplicated ones, and an actual ordinary on button would make more sense.
    • It could be that the multitool simply visualises the actual complicated workings of a Combine mainframe in the holographic puzzle form, allowing Alyx to brute force the authorization code by solving the puzzle. Also the Combine computers are shown to be largely organic, so the inner code, or "thoughts" could work in such visual manner that it becomes a puzzle to another thinking being, contrasted with human computers which are just a lot of complicated math.
      • If it can perform a process as complex as translating all that to a simple visual puzzle, then it'd easily be capable of just solving the puzzle itself.
      • The tool itself is just a machine, and probably isn't allowed brute force the answer, requiring human input. Also Alyx's multitool is impressive but it's not meant to be perfect, perhaps the one seen in Half-Life 2 had been perfected to such level?
    • Simply put that puzzle thing is a backup access system that's supposed to be projected for a Combine soldiers if their connection to the Citadel is not working. The lock is meant to keep out unintelligent creatures like the zombies that can't figure out more then regular humans who don't have the right tech to view the locking system to begin with. One of many security improvements once the Citadel is complete will be swapping to pure remote access.
      • Why wouldn't they just make it remote access from the start? Hello? Bluetooth?
      • With the Citadel still incomplete having constant uninterrupted access is unlikely to work and Overwatch doesn't want to give recently recruited soldiers unrestricted access. Remote access is the primary means of opening them already, the holographic lock is simply in case of outages.
    • It also makes sense that it'd be a lock in the same sense that matching the symbols is like fiddling with the tumblers of a real lock. A Combine could probably just walk right up to the machine, wave a badge or something similar, and it'd work right away. Alyx, being an ordinary human, has to use her multitool to 'pick' the 'lock'.
      • Then why not just have a capcha "click here to verify that you're not a zombie" system?
      • This is the Combine equivalent of that. Finishing these puzzles is so relatively trivial it's the simplest thing they could come up with that fell above Zombie intelligence.
    • It's a video game.
    Wooden boards 
  • What sort of crap-ass nails are being used in all these boarded-up doors that a zombie can't rip them off, but an ordinary human can quite casually?
    • It's all about body mechanics, the zombies are strong but incredibly dumb. They'll literally walk right into a spinning blades if allowed. Humans can use angles and physics to their advantage thanks to our higher intellect. So for example not just yanking on a board but ending it up and down to loosen the nails.
    Alyx's memories 
  • Did Alyx have her memory of G-Man erased before the events of Half-Life 2, or is there some complex funny business going on?
    • Alyx having her memory erased is the most likely explanation. The stinger shows that the events of Half-Life 2 still played up until the advisor attack at the end, which wouldn't be possible without Alyx. In Episode 2 G-Man uses Alyx to deliver his message to Eli and she doesn't seem to remember doing it afterwards, so he does have the ability to alter her memory.
    • G-Man travelled back in time, intentionally allowed himself to be captured, and set in motion the events of Half Life: Alyx in a sort of branched timeline. These events only happened because of the G-Man. The Combine detected his presence and quickly contained him. In the original timeline, none of this occurred.
    What Eli witnessed 
  • Did Eli see his daughter kill the Advisor or did he put together G-Man's involvement by seeing him over on the stairway to the right?
     Alyx's past and present 
At the end of the game, Alyx is put into stasis by G-Man, after he brought her five years into the future. But the post-credits scene hints that the "future" Alyx disappeared suddenly, having been present until that point. So which Alyx was taken? Younger? Older? A timey-wimey mixture of both?

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