Jonathan is a playable character along with Joseph Joestar, both representing the JoJo's Bizarre Adventure franchise in the game.
Jonathan's color scheme is the same one from the TV Anime series. Both Jonathan and Seiya (from the SAINT SEIYA franchise) share the same battle theme, called "Brave Soldiers".
He also makes brief appearances in the game's opening sequence, as he can be seen alongside other Jump heroes, and at some point watches Gintoki race against Ryotsu (from KOCHI-KAME franchise).
Moveset
Jonathan's moveset consists of most of his attacks featured in Part 1. His main gameplay style involves regular combos ending with his Sunlight Yellow Overdrive (it can be extended for more damage up to 49 hits), his Zoom Punch as a long-range attack, a ranged variation of his Scarlet Overdrive wave on the floor, and his Luck & Pluck sword return as a 3 Hit-Combo that can be used to inflict large amounts of damage. Aside from similar attacks from his All-Star Battle moveset, Jonathan's new moves include him using a spear (the same one he used in the Joestar Mansion to fight Dio) and a charged dash attack that continues until he hits his target with his shoulder.
His special move unleashes a stronger version of the Sunlight Yellow Overdrive, followed by a Scarlet Overdrive that launches the opponent away. Some of his famous JOJO poses appears as taunts and intro/victory poses.
(Keep tapping to strike repeatedly)
+ 
+ (After hitting the target, press to fire up to 3 extra shots)
during a Victory Burst
(Hold to charge) + + / / 
while dashing + / + 
/ + 
/ + 
while jumping while jumping + just before sustaining an attack or at the moment of landing after being thrown into the air or knocked off your feet when voltage gauge is full
to an opponent that has been sent into the air by an ally to an opponent that has been knocked down into the ground after an ally's successful combination attack simultaneously to attack an opponent that has been knocked down by a successful cross chainStory Mode
Jonathan's role during the Story Mode is limited to quick appearances. During Toriko's team arc, the player takes control of the duo Gintoki Sakata (from the GINTAMA franchise) and Boa Hancock (from the ONE PIECE franchise), as they both claim to have seen a person walking across the water towards their direction. The person is revealed to be Jonathan, who challenges the player's team, claiming that he's training to defeat Dio (likely a reference to Zeppeli's Ripple training, when they followed Poco by running over the water). After the battle, Jonathan appears surprised he lost the match and says he still needs more training, then introduces himself by saying "My name is Jonathan....Jonathan Joestar."
Interactions
Despite not having any specific conversation or interaction with Joseph, they both appear as rivals in one of the promotional videos for the western version of the game, J-Stars Victory VS +, with their battle titled "WHEN GRANDSON MEETS HIS GRANDFATHER!". Oddly enough, the trailer begs the question "IS THE FLAME OF YOUTH STRONGER THAN THE WISDOM OF AGE?", which erroneously implies that Jonathan, as Joseph's grandfather, is much older than him, as well as alive by the time Joseph is 18 years old, rather than the game's incarnation of him being only two years older than his grandson as the two are from completely different time periods.