How does one defeat an enemy's True-Name Nemesis?
Protection doesn't provide perfect invulnerability against your stuff. The reminder text on the card lists specifically all of the things that you can't do. Here are some ways to deal with an opponent's True-Name Nemesis:


Decrease your opponent's creatures' toughnesses. For example, if you play Elesh Norn, Grand Cenobite, your oppenent's creatures will get -2/-2, so the True-Name Nemesis will have less than zero toughness and die due to a state based effect.
Destroy or exile all creatures. If you play Wrath of God, all creatures will be destroyed, including the True-Name Nemesis. There's nothing that say's that it can't be destroyed by effects you control.
Force your opponent to sacrifice a creature. If you play Consuming Vapors, they'll have to sacrifice a creature. You can force them to sacrifice the True-Name Nemesis if you get rid of their other creatures.
Prevent it from attacking. You can either make it very expensive to attack you, with Norn's Annex, for example, or just prevent it entirely with Blazing Archon.
Remove its protection. If you play Polymorphist's Jest, Sudden Spoiling, or Humility, all of your opponent's creatures will be 2/2 Frogs with no abilities, including the True-Name Nemesis. Then you can get rid of it like any other creature.
Make damage unpreventable, then deal mass damage. For example, you could play Everlasting Torment, then Anger of the Gods.
Outpace your opponent. If you have enough power on the field, you can either kill kill them faster than they can kill you, or force them to keep the True-Name Nemesis untapped as a blocker.
Prevent it from entering the battlefield in the first place. You can counter it with any of a number of counterspells, name "True-Name Nemesis" with Nevermore, Meddling Mage, or Voidstone Gargoyle, cast Iona, Shield of Emeria and choose "blue", or just cast Llawan, Cephalid Empress.
Force it to block with an effect that destroys blocking creatures. For example, if you enchant an Engulfing Slagwurm with Lure and attack, the True-Name Nemesis will be forced to block if able, and it will be destroyed.
Make it deal damage to itself using Wave of Reckoning.