On Gotham 3×18 “Light The Wick,” Nygma and Penguin had the reunion that everyone knew was coming, and yet no one was prepared for.
Penguin made it his mission on Gotham 3×18 “Light The Wick” to get Nygma from the Court of Owls. Determined to get his revenge, Penguin isn’t about to let the Court get in his way. So he corners Gordon and threatens asks him to get a pre-programmed phone to the Court so they can negotiate.
Gordon does talk to Kathryn about it, but she unsurprisingly doesn’t care. Instead, Gordon ends up using the phone as a way to lure Penguin to help him when Kathryn wants to test out the new weapon.
Penguin does get in touch with the Court when they come after him for killing their assassin. He’s thrown into a cell at their dungeon right next to Nygma! Still thinking that Penguin is dead, Nygma is shocked to see his former best friend. Penguin’s reaction to seeing Nygma is more like blinding rage. Both their reactions were very intense and sent their fans into a frenzy on Tumblr.