If there was another animated season of BB, this is how I'd do it:
Batman Beyond
Season 4
Episode #1- Targeted
Batman travels to Metropolis in pursuit of the Kobras, only to find they've hired a protector, Curare. Meanwhile, Xander attempts to clone his queen, Max.
Episode #2- The Demoness
When the entire JLU turn up missing, Batman goes off in search of his comrades. However, he calls upon the aid of Jason Blood/Etrigan when he finds the JLU's captor, Felicia Faust, daughter of the powerful Felix Faust.
Episode #3- Dark Ally Part 1
Commissioner Barbara Gordon and Batman are shocked when a new Batgirl appears to help Terry apprehend Mad Stan. Following the new crime fighter on her escapades, Batman finds her to be Melanie, formerly of the Royal Flush Gang. However, when Bruce Wayne does some digging, he learns she was trained by his former partner, Dick Grayson!
Episode #4- Dark Ally Part 2
Visiting him in Bludhaven, Batman finds Dick Grayson running a superhero training camp. After refusing to see Bruce Wayne or Commissioner Barbara Gordon, the former Boy Wonder and the new Batman become allies when one of the superheroes in training is found to be Stalker.
Episode #5- Spare Parts
Attempting to lure Zeta into a trap to adapt his own suit, Shriek kidnaps his companion, Ro. However, the reformed robot calls upon Batman to help him confront the Master of Sound.
Episode #6- Family Ties
Bruce Wayne suspects the worse when he learns that Terry's girlfriend, Dana Tan, might have a strange connection to Inque.
Episode #7- Arch Nemesis Inc.
The JLU once again ally themselves with Batman as the newer, deadlier Injustice Gang has a new member, Earth Mover.
Episode #8- Goosebumps
Only the new Batgirl can save Batman when Spellbinder and his accomplice, Dr. Jonathan Crane a.k.a. the Scarecrow, force the Tomorrow Knight to fear himself.
Episode #9- Struck By Lightning
It appears that over the years, Maxie Zeus has led the good life on his own self-styled Mt. Olympus in Greece. However, trouble starts for Batman when Maxie's estranged son becomes Hercules and declares revenge against his uncle, Hades. As before, the Zeus family believes Batman to be Hades.
Episode #10- Lovesick
After thwarting one of Dr. Cuvier's splicing schemes, Dana accuses Terry and Max of spending too much time together. The relationship is really put on the rocks when Dana and Max are kidnapped by the Kobras. Meanwhile, Selina Kyle shows up to tie up loose ends with Bruce Wayne.
Episode #11- Afterglow
After a nuclear fallout in Kaznia, Blight returns to exact revenge on Bruce Wayne, Batman, and Paxton Powers.
Episode #12- Twisted Past Part 1
Gotham seems almost too quiet for once when the Jokerz seem to disappear. Dick Grayson finally meets up with Commissioner Barbara Gordon when her husband, Sam, discovers his training camp. However, the Jokerz return in the form of the more organized Facerz and Dick provides a startling revelation.
Episode #13- Twisted Past Part 2
Returned from his self imposed exile, Two-Face and his Facerz all but take over Gotham City. However, with Bruce Wayne and Commissioner Barbara Gordon "commanding the troops" from the Batcave and Batman, Batgirl, Max, and the returning Nightwing in the streets, the battle for Gotham City isn't over yet!