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Sabotage and Counterculture both interact with stacked cards. When interacting with single stacked cards, you may only target the very top card of a stack  

NO! Sabotage and Counterculture can only target cards stacked onto a building, not the building itself. Even if a building has no cards stacked on it, it still can not be targeted.  

Shuffle the discard pile into a new Play Deck to draw from. If there is no discard pile left to shuffle, and you try to draw a card from an empty deck, then your countries enter a financial crisis. In other words… 

…a missile is immediately launched at every player, starting with you. Yay! Now you have a discard pile to shuffle into a play deck to draw from! (no response systems are launched in retaliation.) 

if you just Stacked the 4th card on your Shuttle Program then it’s clear you could win next turn. You could create another target for players to consider attacking instead of you by playing another player’s second Peaceful Protest for them! 

Players may choose to launch a missile at their own City and/or Sabotage/Invade their own Buildings. Upon triggering their own Response System(s), the player gets to choose the Response System 

missile target. In other words, a false flag operation.