Not sure why everyone is giving you examples on using the KeyState command. While it's used more often and has better functionality, it wasn't the question you had asked, nor does it answer what was going right/wrong for you... except for the fact that anything other than entering 1 will cause the game to end (not just 2). But in keeping with the commands you were learning about there are other ways to ensure only 1 or 2 are acceptable choices.
Your code was fine. You just weren't seeing the last print statement because the program would end and close before you could see it. Since you really don't have a game-loop at the moment,, the best that I could do to show you that your code was working,, was to put a wait key command at the end. this prevents your app from closing until a key is pressed.
I also added an end command to else condition. If it wasn't there the program would execute the cls and the following print command after printing "Game Will End".
Print
Print "We need you to investigate "
Print "Will You Investigate"
Input "Press 1 for yes or 2 for no and hit enter: ", FirstMission
If 1=FirstMission
Print "Ok Then Lets Go"
Else
Print "Game Will End"
wait key
end
endif
cls
Print "Lets get you in to the Chopper"
wait key
Also, while it works fine this way. Most often you will find the variable on the left of the evaluation
if FirstMission = 1
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