@ABSTRVCT If you think you can disable or enable plugins dynamically by modifying the plugin.js like Zeriab described - that won't work as easily as you might assume, which is why Zeriab couldn't see a reason for you to do that.
In 90% of all cases, changing the active plugins in the plugin manager still requires the player to start a new game for the newly activated plugins to work correctly, as they make older savefiles incompatible.
I won't go into details as to why that is the case, but it still applies even when you change the plugin.js by another plugin instead of manually in the plugin manager.
So if you have a plugin change the plugin.js while the game is running, you will get errors if the changed plugins can't handle those dynamic changes.
And to prevent that, the player will still be forced to start a new game, abandoning the current one.
There are only two ways how this method can work - either if the plugin is written in a way that allows it to work without a new game (as most are not), or if you want to enable a plugin for a future new game only after the player has solved the game once (similiar to "new game plus" plugins)