Diamond and Pearl 2
In a ploy similar to gold/silver, team Galactic can't deal with their leader being missing, and so they enslave another legendary to break the fabric of time and space in an attempt to cross the rift and reach Cyrus. In addition to causing temporal/spatial anomalies across Sinnoh(cool puzzles to figure out to progress), it turns out that they opened the wrong kind of rift, inviting a far sinister force to invade. In order to fix this mess once and for all, you have to find your way into the actual distortion realm, only to find that Cyrus died a long time ago. You instead find a cool new legendary pokemon (Giratina mysteriously absent) and with its help you defeat Galactic again, and seal the rift they opened, (but not before fighting an UB that escaped). You then go on and defeat the elite four, roll credits.
Part 2: Through a series of events you find out that Giratina itself had traversed from the distortion realm into this mysterious alternate realm that Galatic had discovered, in an attempt to defeat the army itself. You need to now enlist the help of the new legendary you caught to once again open this rift and help save Giratina. Things are more civilized than previously thought, and you end up having to fight 8 more gyms in this new world to finally reach Giratina. Big climactic fight, bbeg of the new world is defeated through the power of friendship, cue credits again. There's a cool alt-world battle park that has randomized maps with varying objectives. (defeat enough trainers, catch enough pokemon, find enough hidden items, gather enough berries, etc.)
