Bool function not working?

function fire() -- Pew pew
    local mWasMissileFired = false

    if mWasMissileFired == false then
        mWasMissileFired = true
        main.Parent.Safe.Missiles.Missile:BreakJoints()
        wait (0.05)
        main.Parent.Safe.Missiles.Missile.Launch.Disabled = false       -- This is not a good way to run scripts
    else
        print 'Worked!'
        main.Parent.Safe.Missiles.Missile2:BreakJoints()
        wait (0.05)
        main.Parent.Safe.Missiles.Missile2.Launch.Disabled = false  -- This is not a good way to run scripts
        mWasMissileFired = false
    end
end

I recommend putting the whole launch missile script as a separate function, then add a plethora of boolean variables (assuming you only want the 2 missiles to fire and those 2 missiles only. You could add a regen function to restart the whole process):

function Launch()
    --[[ Your launch function here ]]
end

function Launch2()
    --[[ Your launch function here ]]
end

function fire() -- Pew pew
    local mWasMissileFiredOnce = false
    local mWasMissileFiredTwice = false
    local debounce = true
    if mWasMissileFiredOnce == false and mWasMissileFiredTwice == false and debounce == true then
        debounce = false
        main.Parent.Safe.Missiles.Missile:BreakJoints()
        wait (0.05)
        Launch()
        mWasMissileFiredOnce = true
        debounce = true
    elseif mWasMissileFiredOnce == true and mWasMissileFiredTwice == false and debounce == true then
        debounce = false
        print 'Worked!'
        main.Parent.Safe.Missiles.Missile2:BreakJoints()
        wait (0.05)
        Launch2()
        mWasMissileFiredTwice = true
        debounce = true
    elseif mWasMissileFiredOnce == true and mWasMissileFiredTwice == true then
        return nil          -- Ehh, this last 'elseif' statement isn't really needed, but oh well
    end
end

But assuming that you don't want a regen function, that you wanted to reload the missiles after a set amount of time or something. Well, you'd have to get rid of the BreakJoints() method and instead make a new part as a missile.

mWasMissileFiredOnce = false
mWasMissileFiredTwice = false
debounce = true
FinishedShooting = script.Parent.FinishedShooting
FinishedShooting.Value = false
-- Setting these variables to global (outside of a code block) will let other functions manipulate the variables

function Launch()
    --[[ Your launch function here ]]
end

function Launch2()
    --[[ Your launch function here ]]
end

function fire() -- Pew pew
    if mWasMissileFiredOnce == false and mWasMissileFiredTwice == false and FinishedShooting == false and debounce == true then
        debounce = false
        main.Parent.Safe.Missiles.Missile:BreakJoints()
        wait (0.05)
        Launch()
        mWasMissileFiredOnce = true
        debounce = true
    elseif mWasMissileFiredOnce == true and mWasMissileFiredTwice == false and FinishedShooting == false and debounce == true then
        debounce = false
        print 'Worked!'
        main.Parent.Safe.Missiles.Missile2:BreakJoints()
        wait (0.05)
        Launch2()
        mWasMissileFiredTwice = true
        debounce = true
        FinishedShooting = true
    elseif mWasMissileFiredOnce == true and mWasMissileFiredTwice == true then
        return nil          -- Ehh, this last 'elseif' statement isn't really needed, but oh well
    end
end

FinishedShooting.Changed:connect(function (Value)
    if FinishedShooting.Value == true then
    wait(10)
    mWasMissileFiredOnce = false
    mWasMissileFiredTwice = false
    FinishedShooting.Value = false
    end
end)
-- For this to work, you have to have a bool value named as "FinishedShooting" with it set to false at the parent of this script.

So I used your first option as the second one ended up breaking the rest of the script (Don't know exactly why, think it was something regarding the Boolean not being local) but for some reason it just keeps running the Launch() function and doesn't move onto Launch2()

*Note chached "Missile" to "Missile1" dissolved "Launch" script & merged with Launch() functions

function Launch()
        wait (0.2)

        main.Parent.Safe.Missiles.Missile1.Fired:Play()

    local a = Instance.new('BodyThrust')
        a.force = Vector3.new(0, 4105, 125000)
        a.location = Vector3.new(0, 0, 0)
        a.Parent = main.Parent.Safe.Missiles.Missile1

    wait (0.5) -- Safety percaution to avoid self destruction 

    main.Parent.Safe.Missiles.Missile1.Explode.Disabled = false
end

function Launch2()
    wait (0.2)
        main.Parent.Safe.Missiles.Missile2.Fired:Play()
    local a = Instance.new('BodyThrust')
        a.force = Vector3.new(0, 4105, 125000)
        a.location = Vector3.new(0, 0, 0)
        a.Parent = main.Parent.Safe.Missiles.Missile2
    wait (0.5) -- Safety percaution to avoid self destruction   
    main.Parent.Safe.Missiles.Missile2.Explode.Disabled = false
end

function fire() -- Pew pew
    local mWasMissileFiredOnce = false
    local mWasMissileFiredTwice = false
    local debounce = true
    if mWasMissileFiredOnce == false and mWasMissileFiredTwice == false and debounce == true then
        debounce = false
        main.Parent.Safe.Missiles.Missile1:BreakJoints()
        wait (0.05)
        Launch()
        mWasMissileFiredOnce = true
        debounce = true
        print 'Done1'
    elseif mWasMissileFiredOnce == true and mWasMissileFiredTwice == false and debounce == true then
        debounce = false
        print 'Worked!'
        main.Parent.Safe.Missiles.Missile2:BreakJoints()
        wait (0.05)
        Launch2()
        mWasMissileFiredTwice = true
        debounce = true
        print 'Done2'
    elseif mWasMissileFiredOnce == true and mWasMissileFiredTwice == true then
        return nil          -- Ehh, this last 'elseif' statement isn't really needed, but oh well
    end
end