PokéBase - Pokémon Q&A
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After years of having a dry internal battery, I finally looked up videos on how to replace it and did it successfully. I know this because I no longer receive the message that "The internal battery has run dry. The game can be played. However, clock-based events will no longer occur." The clock itself in my room works, as well as the tides in Shoal Cave, but I would like to be able to get berries again from the berry master, lottery tickets in Lilycove, and especially have battles at my registered friends' secret bases. Does anybody have more information on this? Are the Shoal Cave tides and Berries separate from CPU-related events in the game? Is there any way I can reactivate the latter again without having to start a new game? I'd even consider a hardware alteration to the game if necessary, now that I'm more familiar with soldering on a new battery.

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Are you sure you've waited at least 24 hours?
lol i cant believe you changed the battery, all i did was save and it went away :P
Changing the battery is necessary for the game to run timed events when it dies. Plus, just because you "fixed" it by saving the game (which isn't how it's supposed to work), doesn't mean everyone else will have the same results.
I appreciate comments so far but I'd still like a real answer. I've waited probably 2 weeks and they still say to come back later/tomorrow. I discovered today that the old man in Pacifidlog says that in 2321 days he'll have a good TM for me. That's over 6 years! I wonder if that's how long the internal battery has been dead. Also, the rocket scientist in Mossdeep says it's successful launch no. 1.

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Okay, after some research, I believe I have figured out your problem, and that's the Berry Glitch.

When your game starts, it sets the RTC (Real Time Clock), and the set date is always January 1st, 2000. Each day, month, year, etc. is counted from there instead of having an in-game calender. However, after one year has passed, all time-based events freeze for another year. This occurs with all events that happen once a day (the Berry master, lottery tickets, etc.) However, this part in particular may be what you're looking for:

Cartridges that have had their battery replaced may also experience similar problems. When the supply of power from the battery is interrupted, the RTC is reset to January 1, 2000. As with the Berry glitch, this reset causes all scheduled calendar-based events to be frozen until the RTC reaches the expected value, which may take many years. This can be solved by starting a new game, or (with additional hardware) by altering the timestamp stored in the save file so it is lower than the RTC value, or by setting the RTC forward so it is greater than the save file timestamp.

The only way to fix this glitch without outside devices is if you start a new game, then link two gameboys together, one with LeafGreen, FireRed or Emerald in it, and one with your Ruby in it. Follow these instructions:

  1. Load FireRed, LeafGreen, or Emerald until the title screen is displayed.
  2. Press the Select and B buttons. After the new screen loads, press A.
  3. Insert the Link Cable so that the system that the FireRed, LeafGreen or Emerald game is connected to the Player 1 cable port and the Ruby or Sapphire game is connected to the Player 2 port. Once this is done, press A.
  4. Turn on the device with Ruby or Sapphire while holding the Start and Select buttons.
  5. Refer to the FireRed, LeafGreen or Emerald game display for further instructions. The patch should be transferred at this time.

For more information, please click here: http://bulbapedia.bulbagarden.net/wiki/Berry_glitch

I hope I helped!

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Thank you very much. I had heard about the Berry Glitch, but never fully looked it up until now. I think that's exactly what I have, and may have to just wait 2321 days until it's fixed because I don't have any other versions of the game.