I’ve found that even after enemies detect you, you’ll still be able to run up to them and quickly tap the button to take them down before they can even fire at you. You’ll be able to perform takedowns from cover once an enemy is near your position, and you can also do it even when the enemies have been alerted to your presence. After using it once, there will be a short cooldown timer that has to count down before you can use that ability again, so make sure to use it wisely. However, do take note that you can’t just perform takedown after takedown. On PC, you’ll want to tap the Q button once you’re near an enemy to perform a takedown. This will allow Jensen to take out the enemy, either lethally or non-lethally. Just like in the first game, the only way to perform a melee attack is by getting up close and personal with an enemy and tapping the ‘Takedown’ button. There just simply isn’t an option to do that. Unfortunately, when you’re first starting out in Deus Ex: Mankind Divided, you won’t be able to perform melee attacks.
