So, I have the code, its not done, but all i want it to do is display one alert box if I write the word \'help\', and say something else if anything else is entered.
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The reason why it always pops up is that reply === 'help' || 'Help' evaluates as (reply === 'Help') || ('Help'). The string literal Help is always truthy in Javascript hence it always evaluates to truthy.
To fix this you need to compare reply to both values
if (reply === 'help' || reply === 'Help') {
...
}
Or if you want any case variant of help use a regex
if (reply.match(/^help$/i)) {
...
}