Title says it all; how do I play the mission packs.

In the directory are readme files that say (copy and paste);

"To run Quake II Mission Pack: The Reckoning, copy this folder
and other files into the quake II directory, replacing the
current xatrix folder. *** THIS WILL ERASE YOUR SAVED GAMES AND
CONFIGURATION ***

Run using reckoning.bat"

What the Hell does that mean? It's *already* in the Quake 2 directory. Copy it from where it is to... where it already is?

I don't get it.

EDIT: What the hell is a reckoning bat and should I be scared of it? (There are no .bat files in any Quake related directory.)

There is no such readme files in Quake 2 aka Quake 2 Quad Damage aka Quake 2 (Original) (as it is titled in GOG Galaxy)
Cant say for sure for Quake 2 Enhanced aka Quake 2 (as it is titled in GOG Galaxy).

Looks like readme from not thebmission pack but some mod-pack 3rd party sourced. Or maybe some warez sourced mission pack. Made for sourceports 3rd party. Shouldnt be such file in GOG.

For Quake 2 Enhanced Mission packs started from main menu. For original quake 2 default launch link open Quake 2 launcher from gog that provide chose which start (can be edited in ini).
Are you sure you download GOG and didnt download above anything 3rd party "must have patches"?

There is 3 entries for Quake 2 on GOG - for Enhanced, for original and for RTX. RTX require some set-ups and base game installed first. No bat files in any of them and they not needed for original and enhanced. But they needed for RTX or you can copy-paste not just files which RTX setup exe copy but whole quad damage folder to RTX without replacing. Then edit Q2Launcher.ini file and Windows REGEDIT to make Q2Launcher.exe in RTX folder use RTX exe and not original one. StartbRTX or mission packs from Q2Launcher.exe.

Again. Enhanced and Original launch links lead to menu to chose what mission pack you want to start. If that not happen for you you install RTX edition or not the GOG at all or did install something 3rd party above before trying how vanilla installation working and now that should be fixed.
RTX edition require set-ups to include base game, addons, music, videos. Original and Enhanced already preconfigured.
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as for bat file it is text based file with command line inside. It is one of executable types (exe is not the only one executable). You can edit it or create with Windows WordPad. It is alternate way for RTX version or Retail disc editions without GOGs launcher. Default links use +game xatrix or similar, bat file is same as .lnk have command to start quake2.exe with +game xxxx argument.