- Jonathan vs Dio Brando (At Joestar Mansion; child)
- Jonathan vs Dio (when Dio becomes a vampire)
- Jonathan vs Jack the Ripper
- Jonathan & Zeppeli vs Dio
- Jonathan vs Bruford
- Jonathan vs Tarkus
- Jonathan vs Dio Brando (final battle)
Jonathan appears in the game's intro, along with Jotaro, Josuke and Joseph (Part 3) as part of an image of previous Joestars representing how Giorno inherited their "golden soul." Jonathan originally did not appear in this scene in the manga.
This small appearance marks Jonathan's first appearance in video games media.
Jonathan is the main playable character in this game. Throughout the game the player will control many different versions of him with wildly differing movesets.
The player starts off Story mode as Young Jonathan, defending Erina Pendleton from bullies harassing her. Here, his moveset only consists of punches and kicks. While in the manga Jonathan lost this fight, the game includes an alternate scene should the player defeat the bullies, where he helps Erina back up on her feet only for him to be struck back down when the bullies realize who he is. The second chapter features "Boxing Gear" Jonathan in a match with Dio, also without special moves. Much like the previous level, the player can change how the fight went from the manga by having Jonathan beat Dio, although the resultant scene has Dio turn everyone against Jonathan anyway by claiming Jonathan hit him with a rock. The last level played as young Jonathan is against young Dio, when Jonathan attacks Dio in a fury over what he did to Erina. The player moves on to the "adult" Jonathan chapters, and it is around the Ogre Street level that the player earns his "strong kick" special move. When the player fights a newly-made vampire Dio, Jonathan starts off with a spear, though he loses it afterward.
The boss battle with Wang Chan allows players to use Jonathan's Ripple ability for the first time, allowing him to destroy zombie-type enemies. The player also earns the "Turquoise Blue Overdrive" special move to use against Bruford in the first underwater boss battle, and in the second phase of the battle, the player earns his Sunlight Yellow Overdrive super move. The player then moves on to playing as a shirtless Jonathan against Tarkus, with the added bonus of having a constantly regenerating Ripple meter thanks to Will A. Zeppeli passing on his Ripple ability to Jonathan. The closing stages of the game has Jonathan wielding the sword of LUCK & PLUCK as well as granting him the Scarlet Overdrive special as well. The very last level has the player use a fatally wounded and dying Jonathan, with very little health left and only enough energy for one last Ripple attack, in an attempt to recreate the final scene of Part 1.
During EXTRA BATTLE and 77 RINGS KNIGHT MODE, Jonathan is playable with both "Luck & Pluck" and without it. His Tuxedo version is also playable, but it must be unlocked by beating the STORY MODE once.
Jonathan appears as a support and help character in the game. His 2 Koma support summons him, after which he headbutts his target and performs a combo on them. His 3 Koma support involves him tossing Ripple roses at the enemy, striking them with LUCK & PLUCK and performing a Scarlet Overdrive on them. His help koma gives the character 1 SP bar more after being defeated.
He serves as an ally boost with DIO, mocking his classic line "it's useless!" and Mutou Kazuki (from Busou Renkin), by saying he feels the sun's power in Kazuki (since they need the sun's light in some of their attacks, Jonathan's Ripple and Kazuki's lance).
Jonathan returns as a playable character in the PS3 game. He was confirmed along with Will Anthonio Zeppeli and Johnny Joestar. As a Ripple-user character (along with William, Joseph [Both Parts 2 and 3], Caesar, and Lisa Lisa), Jonathan can recharge his Heart Heat Gauge through "Ripple Breath" by holding down the Style button, performing a famous JoJo pose, as well as deliver enhanced versions of skills if Style is inputted in place of normal attack buttons.
Jonathan's moveset mostly comprises of the Ripple-based moves he had used in the original manga.
- Tackle: Jonathan lunges forward shoulder-first. If not blocked, the opponent is sent into the stage wall. Every single one of Jonathan's skills can be performed instantly following this move, though Scarlet Overdrive has the best chance of landing.
- Zoom Punch: Jonathan extends his arm and punches at medium range, stunning the opponent and leaving them vulnerable. Every single one of Jonathan's skills can be performed instantly following this move. (Comboable)
- Sendo Ripple Overdrive: Jonathan shoots a wave of Ripple energy along the ground in a low attack. This skill deals more damage can knock the opponent into the air if Ripple-enhanced. (Ripple-enhanced Comboable)
- Overdrive Barrage: Jonathan slides forward and rapidly punches, finishing with a small uppercut. This move deals more damage and knocks the opponent into the air on the final hit if Ripple-enhanced (Ripple-enhanced Comboable). This move is able to initiate a Rush Mode struggle with Power-Type Stand users, making Jonathan the only non-Stand-Style character to be able to do so.
- Scarlet Overdrive: Jonathan delivers an instant short punch immediately followed by a flaming rising uppercut with the other hand in a classic "Shoryuken"-style move, doubling as an anti-air. This move cannot be Puttsun Cancelled once Jonathan leaves the ground. The opponent will fly higher and take more damage if Ripple-enhanced. (Comboable)
- The Sword of Luck & Pluck: Jonathan leaps forward, sword in both hands, and unleashes three wide swings, with the final, downward swing grounding the opponent. This first hit is a middle attack that cannot be blocked if the opponent is crouching (Comboable through Puttsun Cancel). If the move is Ripple-enhanced, its damage is increased Jonathan can only be interrupted by Throws and HHA/GHA.
- Throw - I will protect my father!: Jonathan picks the opponent up by one hand, holds them over his head, and throws them to the ground.
- Special - "This is my final Ripple!": Jonathan can spend a stock of his Heart Heat Gauge to perform this move, which allows him to rise again after his health hits zero, with increased attack power and defense as well as all of his skills permanently changing to their Ripple-enhanced variants, although his Heart Heat gauge is disabled entirely. If he's struck by "Kosaku Kawajiri's" GHA, Bites The Dust when this skill is activated, Jonathan will lose it but regains his HHG, assuming he has enough health to survive.
- Heart Heat Attack - "Who'll be the last one standing?!": Jonathan's HHA is the variant of Scarlet Overdrive he used to defeat Dio in the closing stages of Part 1. Jonathan spins as his hands are engulfed in flames, before diving forward, both fists extended. If the opponent is hit, the two-handed strike will hit them in the abdomen. Jonathan then punches through his opponent with a fiery Ripple-charged fist to send them flying.
- Great Heat Attack - Sunlight Yellow Overdrive: Jonathan executes the very move that he used to defeat Bruford beginning with a very fast kick. If the kick lands, the opponent is hit in the abdomen, before Jonathan proceeds to pummel them at different angles and knocking them into the air, all while reciting his signature lines. After charging an immense amount of Ripple energy, Jonathan unleashes a rapid flurry of punches into the opponent as they fall towards him, ending with them spiraling away after a two-handed crossing punch.
Jonathan has many alternate costumes, all taken from each of the 5 volume covers in which he appears. Besides the Part 1 characters, Jonathan has a special intro with DIO's Part 3 incarnation, where Jonathan expresses horror at Dio seemingly being alive again while DIO remarks on "JoJo"'s appearance before him possibly being "a challenge from the past."
Jonathan is a playable character along with Joseph Joestar (Part 2), both representing the JoJo's Bizarre Adventure franchise in the game.
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's 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, following with a Scarlet Overdrive that launches the opponent away. Some of his famous JOJO poses appears as taunts and intro/victory poses.
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."
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).
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.
Jonathan is one of the first 3 available characters the player must choose to be his first team leader (alongside Joseph and Jotaro). Several of Jonathan's appearances appear as Medal Strikers.
Jonathan's FINISH move consists of an animation wherein he strikes his enemy with several punches in a second while his Special Level 3 Leader ability has him use Scarlet Overdrive on all enemies on the field.
Jonathan was confirmed for the game alongside Zeppeli and Speedwagon.
Most of his moveset and character model remains the same from All Star Battle. New additions to Jonathan's attacks includes him using the spear he attacked Dio with shortly after his transformation as a Powerful Attack. Several of his new combos and sidesteps are now based on his boxing skills (displayed during his childhood in Part 1).
As a Ripple User, Jonathan has a Ripple Gauge that determines the strength of his attacks. Filling up the gauge will automatically empower his Normal and Powerful Attacks, and enhance/alter the properties of all his skills. It will also shorten the cooldown time on said skills. Using skills will drain a portion of the Ripple Gauge until there's an insufficient amount to use.
- Style Action - Ripple Breathing: Jonathan performs a pose and Ripple Breathes, filling up the Ripple Gauge. He cannot move and is vulnerable to attacks while doing so.
- Zoom Punch!: Jonathan slides forward and extends his arm to punch at medium range, dealing medium damage to opponents. If Ripple-enhanced, the skill will execute quicker and allow Jonathan to combo from it (Ripple-enhanced Comboable).
- Overdrive Barrage!: Jonathan slides forward and unleashes a short flurry of punches ending in an uppercut. The last hit will send opponents flying. If Ripple-enhanced, the skill will execute quicker, unleash more punches, and receive a damage boost. The skill can be used in mid-air, and its damage is dependent on the how much of the Ripple Gauge is filled.
- Sendo Ripple Overdrive!: Jonathan punches the ground and sends his Ripple spreading out over a wide area, damaging and crumpling opponents caught. If Ripple-enhanced, the skill will execute quicker, have a larger area of effect, and receive a damage boost.
- Who'll be the Last One Standing!: Jonathan spins as his hands are engulfed in flames, before diving forward, both fists extended. If the opponent is hit, the two-handed strike will hit them in the abdomen. Jonathan then pulls one fist back before punching them off, sending the opponent flying as he briefly turns down and looks down. If Ripple-enhanced, the skill make Jonathan invincible during its execution, receive a damage boost, and the speed and distance of the dive is increased. The skill's damage is dependent on how much of the Ripple Gauge is filled.
- EX - Sendo Ripple Overdrive!: Jonathan will be invincible when first executing the skill. The Ripple will be unblockable, and Jonathan's recovery time from the skill is reduced as well, allowing him to combo from it. This is in addition to other benefits granted by the Ripple Gauge.
- EX - Who'll be the Last One Standing!: The skill will execute even quicker than when Ripple-enhanced, will increase the speed and distance of the dive, make Jonathan invincible while he is diving, and receive a damage boost. This is in addition to the damage benefits granted by the Ripple Gauge.
- Trait - My final Ripple...: When Jonathan health hits zero for the first time, if his partner is still alive, he will be granted a decent portion of continuously draining health to continue on it. All attacks and skills are unusable, leaving Jonathan with a special final attack in which he attacks with crossed fingers, dealing considerable damage. Once his health reaches zero once more, or if he successfully lands his final attack, Jonathan will then fall permanently.
- One-in-a-Million Potential: Jonathan must completely fill his Ripple Gauge. (200 Points)
- Father! Grant me your final power!: Jonathan must connect a Powerful Attack as the third step in a mid-air combo. (200 Points)
- I want to become a true gentleman!: Jonathan must successfully execute 5 Combo Breakers. (300 Points)
- I'll knock you until you cry like a little girl!: Jonathan must achieve a collective hit count of 200. (500 Points)
- Own your fear!: Jonathan must Retire an enemy with a Dual Heal Attack. (800 Points)
Dual Heat Attacks
- Solo - Sunlight Yellow Overdrive!: It works the same as the one from All Star Battle, however, most of the speech is removed in favor of several grunts.
- With Zeppeli - "Here comes my Hamon!": The two of them attack the opponent's head, sequentially with a Ripple-charged Zoom Punch from Jonathan and a Sendo Wave Kick from Zeppeli, before they charge up and run up to the opponent and unleash a double Sendo Ripple Overdrive-enhanced Zoom Punch into them, the two reciting the phrase commonly associated with Overdrives.
If fighting against Kars, Jonathan will realize he created the Stone Mask that caused his life so much misery and in his victory quote he states Kars will pay for what he has done. He might also be left in shock at Kars' status as neither zombie nor vampire. This applies to the rest of the Pillar Men.
He is paired with DIO in the Eyes of Heaven Tournament, defeating Zeppeli and Koichi Hirose in the first round and Wamuu and N'Doul in the second. In the semifinals, they defeated Mariah and Esidisi in the first round, but were eliminated by Kars and Pet Shop in the second.
Jonathan is a playable character in the game with many different unlockable statues that are Courage or Unity types.
- In Jump Comics Volume 1, there is a typographical error where Jonathan uses the line 何をするだァーッ (Nani o suru da) instead of 何をするんだァーッ (Nani o surun da). This error was not fixed for 15 years until the 66th printing and has since then been replicated in other works such as Phantom Blood (PS2 Game) and All Star Battle.
- According to an interview with Araki, Jonathan's name was inspired by a family restaurant, "Jonathan's," at which he and his editor would frequently meet late at night to discuss ideas.
- According to JOJO A-GO!GO!, the ability DIO uses during Stardust Crusaders, to create a vision on a crystal ball, is actually a Stand power which awoke in Jonathan's body.
- Jonathan has a similar appearance and physique to Hokuto no Ken's Kenshiro.
- Araki stated in JoJonium Vol. 1 that Jonathan was difficult for him to design. He wanted to create a "first Joestar" that could function as a symbol of purity and dignity rather than a unique, fresh character. However, there were limitations on how he could write the character due to being a "symbol of justice", so Araki found himself unsure where to take the character.
- Jonathan is the only character to appear in every chapter of the respective part they were introduced in, as he is in every chapter of Phantom Blood.
- Due to the concept of the Joestar Birthmark not being introduced until Stardust Crusaders, Jonathan is not shown to have it in the manga. Later adaptations do show Jonathan's birthmark, such as the 2000 OVA during the flashback showing Jonathan's death, or the 2012 anime when he defeats Tarkus.