This is from Cecil's page on the FF wiki, explaining what happens to him in "After"
Seventeen years later, Cecil is seen at Baron castle with Rosa and Cid, with the castle coming under attack. When the Mysterious Girl attacks the castle, he attempts to question her identity but is defeated when she summons Bahamut. He does not reappear until his son Ceodore and the Hooded Man return to Baron, only to find that many of its inhabitants are impostors, who they escape from. It turns out that Cecil has been possessed by the Mysterious Girl when Ceodore's party encounters him again. They are forced to fight him as well as the Eidolon Odin, who comes to his senses and knocks Cecil out of the possession.
As he is nursed back to health, Ceodore joins Rydia, Golbez, Edge, and Luca to take out the Mysterious Girl, who escapes and Golbez calls the Lunar Whale to pursue her. Soon the whole party, including Cecil (who has lost his will to fight), goes into the crater dungeon to defeat bosses emerging from the eight crystals. Then Cecil and Golbez fight a sinister version of the former's Dark Knight form. But as the Dark Knight is about to finish Cecil off, Golbez jumps in to protect him, taking a heavy blow in the process.
Cecil regains his strength and with the help of his family, defeats the Dark Knight. Cecil continues to fight against the forces of darkness, defeating both the Mysterious Girl and her master, the Creator. With peace assured, Cecil returns home to Baron, where he helps train Ceoodore. Even after the events of the game, Cecil is still stronger and wins the sparring match against his son.
(Not said in the paragraph, but Rosa is reffing the final sparring match, so they're all fine in the end)