Moff Gideon spends most of the season in hot pursuit of Baby Yoda, still trying to track him down to experiment on him, presumably in pursuit of enhancing his own power. After a few tries, he's finally successful at kidnapping Grogu and drawing his blood, but soon after, Din Djarin and the rest of their friends come after him to rescue Grogu (and, in Bo-Katan's case, to reclaim the Darksaber). When Gideon goes back on his word to let Din take Grogu and leave, he and Din fight, blade-to-blade, and Din wins, taking Gideon and the Darksaber back to Bo-Katan.
Unfortunately, as Gideon gleefully points out, the fact that Din was the one to defeat him in battle means that the Darksaber's power belongs to him, not Bo-Katan. Gideon is last seen in the custody of Din, Bo-Katan, and their crew.