In the intro of Emelia's story, he's the one to murder her fiancé Ren, however Emelia is the one to be thrown in prison. He then keeps re-appearing during the story as it progresses, however he's never an in-battle opponent.
After escaping prison, Emelia joins Gradius, a secret police force made by ex-criminals, and chases Joker to learn his motives. She learns Joker was working with Trinity, as they were searching for Cube, a mysterious power source. When the current leader of Trinity is overthrown by Mondo, he sends Joker to Yorkland, telling him Cube was located there. Mondo lets Emelia infiltrate his base, and tells her he made a set-up for Joker, as he needed Gradius to get rid of him, as he was becoming a nuisance for Trinity. Emelia finally confronts Joker in Yorkland's church, where she points her gun to him, while he threatens her to give Cube to him. Just then Emelia hears her boyfriend Ren's voice, telling her to shoot the mask. As it turned out, Joker was actually Ren, who got possessed by a mask while investigating Cube. Emelia hesitates, but as Joker gets near she shoots him, taking off the mask and destroying it, thus freeing Ren from the possession.
One confusing thing about this is how anyone could think Ren was dead if he was wearing the Joker's mask all along.
There is another ending, known as the bad ending, the way to get it is to have Emelia find the Purple Eye after defeating the dragon boss in Gnome’s Cave under Baccarat. So instead of freeing Ren, she kills him along with Joker.
