As the clone wars raged on, John and Aayla were given more missions that had them working together. John showed compassion for his men and they respected him, and he respected them, he and Captain Baccara even got along well. They created tactics that only their ships and clones would know what to do. After a few battles of working with Aayla, John began to sense something in her that he only sensed once before, in his deceased wife, and after their victory against the CIS in the Battle of Clondor 4 he approached Aayla and said, "Hey um, Aayla." Aayla turned to look at John she said, "Yes John?" John gathered as much courage he could muster and said, "Would you like to get a drink with me." Aayla blushed at the question, but she said, "Sure, sounds great." John smiled, and the two Jedi made their way to a local Bar to get some drinks.

When the two Jedi entered the bar, the Bar tender stopped them at the door and he said, "Look pal, we don't serve slaves, so have her wait outside." John looked at Aayla, and back at the Bartender and he said, "She is not a slave, she's a Jedi Master." The Bartender shook his head and said, "Doesn't matter, we don't sell to her kind." John looked at Aayla and said, "Forget this, come on Aayla, let's go." The two Jedi then left the bar to find a different place to get a drink. In the entire town it was the same, any restaurant will not serve slaves species. John could not believe the town, they refused to let Aayla eat in any restaurant. He was extremely mad at the town, but Aayla calmed him down and suggested that they should eat in the cruiser's Mess Hall, John showed a small smile and the two Jedi went to the Bravery's Mess Hall.

Meanwhile on the Separatist's command ship, a man by the name of Count Dooku was discussing the matter about John returning to battle with his master, Darth Sidious. Count Dooku asked his Master, "What if this new Jedi discovers our plans?" Dooku's master, Darth Sidious said in a calm voice, "This Jedi from the Old republic will not reveal our plans, of that I am certain." Back in the Bravery's Mess Hall, John and Aayla were enjoying Bantha Platters. As John finished up, he heard a voice calling to him. John got up and began walking, which made Aayla and the Clone troopers worry. John made his way down the hallways of the Jedi Cruiser. When he turned the next corner, he saw the force ghost of his dead wife. Before he could say anything, his wife's ghost said, "My love, you must return home for them." John's wife's Force ghost disappeared after telling John what she said.

When Aayla found John, he was making his way to the hanger to get into his new Jedi Starfighter. When Aayla asked John where he was going, he told her, "I'm going to my home on Tatooine." When Aayla asked, "What's on Tatooine that you need to go there?" John looked at Aayla and said, before closing his canopy, "Lightsabers." John then powered up his star fighter and flew out of the hanger, so he could make the jump into Hyperspace. Aayla just stood there, not knowing what he meant.

After exiting Hyperspace, John headed towards his home planet of Tatooine. When he landed in Mos Eisley Spaceport, he exited the Hanger where his Starship was and was confronted by two Hutt Cartel Goons. One of the goons asked John, "Will you please come with us, Master Jabba the Hutt would like to speak with you." John wasn't going to kill two Hutt Guards and create an incident, so he agreed, and the Hutt Guards took John to Jabba the Hutts Palace. Besides, Jabba's Palace was where John needed to go anyway.

After a short drive around the Great Mesra Plateau, the transport skiff landed in front of Jabba's Palace. The two guards and John entered the palace and made their way to meet Jabba himself. When Jabba saw John, he said, "Achuta jedai, tah choy? Brings u unko tah Tatooine? (Hello Jedi, to what brings you here to Tatooine?)" John, understanding Huttese, bowed his head and said, "Greetings, you must be Jabba the Hutt, I am Jedi Master John Radmore from the Jedi Order from the days of the Old Republic. I came here looking for something that belongs to me." Jabba chuckled and said, "Choy? Sa, it da u are unko looking che? (What is it that you are here looking for?)" John told Jabba that he is looking for his deceased wife's Lightsabers. Jabba then asked, "Tell je jedai, konchee are doe Lightsabers u seek? (Tell me Jedi, where are the Lightsabers you seek?)" John gave Jabba a smirk and said, "Well, if my memory serves me right, they were left to the Hutt leader who owned this palace back in the days of the Old Republic, I told him that I would return for them when the War against the Sith was over, I told him keep them in the black box with a red symbol on it, the box I gave the Lightsabers in was the box I told them to keep them in." Jabba made a look of surprise and looked at a Hutt guard and nodded his head. The Hutt guard understood what Jabba meant and went to get something. Then, Jabba looked at John and said, "Che centuries, myo family has kept do box da u had described since doe days of doe Old publiko, it was given tah myo Ancestor Toborro by do jedai. Doe jedai said da Tatooine was his bunky dunko world um they belong tah his wife. (For centuries, my family has kept a box that you had described since the days of the Old Republic, it was given to my Ancestor Toborro by a Jedi. The Jedi said that Tatooine was his home world and they belong to his wife.)" As Jabba told John about the box, the Hutt Guard that Jabba looked at came back and brought with him the exact box John described.

When John saw the box, he smiled, and walked over to receive the box, but Jabba stopped John by saying, "However, if choy? U said sa true, then u must answer doe question da doe jedai told myo Ancestor tah ask if do different jedai was tah come um retrieve doe Lightsabers. (However, if what you said is true, then you must answer the question that the Jedi told my Ancestor to ask if a different Jedi was to come and retrieve the Lightsabers.)" John remembered telling Toborro about that, but he did not remember what exactly the question was, until Jabba said, "Choy? Was doe Battle da do young jedai Knight saw two jedai kissing da only doe Husband should know? (What was the Battle that a young Jedi Knight saw two Jedi kissing that only the Husband should know?)" John realized what Jabba the Hutt was talking, so he said, "The answer is…" John paused before saying, "The Battle of Raxus Prime." Jabba the Hutt looked at an old Holo-pad that John recognized, Toborro the Hutt had the exact same Holo-pad. Jabba then chuckled before saying, "Well then, Master jedai, it appears da u are coo u settah u are, u may have doe Lightsabers. Mee hope u find peace, ateema they are bata noleeya do possession. (Well then, Master Jedi, it appears that you are who you say you are, you may have the Lightsabers. I hope you find peace, now they are back in your possession.)" John bowed his head and said, "Thank you almighty Jabba, I will now take my leave." But before he left, John opened the box and saw his wife's Lightsabers, still in good condition.

Back on the Bravery in his private quarters, he gazed at his wife's Lightsabers, a tear began to run down his cheek. John thought to himself, "I guess even though I caught the Sith, I always blamed myself for what happened to her." Just then, the force ghost of John's deceased wife appeared. John said nothing until after he fell to his knees, he then said, "My love, I am so sorry. I should have protected you more." All John's deceased wife said was, "I forgive you John." John looked at his deceased wife with tears running down his cheeks. His wife then brushed her hand against John's check, she then said, "I asked you to return home for my lightsabers, so you can finally put me to rest." When John asked what his deceased wife wanted him to do, his wife told him, "You must go to where they have buried my Body and place the Lightsabers there, only then will I be at peace." John understood what she meant and before he could say that he would do it, his Deceased Wife's Force Ghost Disappeared. John realized what his wife's Force Ghost meant and he got up and made his way to the bridge.

A little while later, John was on the bridge and near the Holo-table, so he could call Aayla. When Aayla answered, John said, "Aayla, I'm putting my fleet under your command until I get back… again." When Aayla asked John where he was going this time, John told her, "It's time I visited my wife." Aayla realized what John was talking about and accepted John's ships under her command until he returned. John then left the bridge to head to the hanger to jump in a shuttle, so he could make the jump to Hyperspace towards Tython. But before John took off in the ship, a squad of Clones approached him and the Sargent in charge said, "Commander Radmore, I'm Sargent Videc, the leader of Viper Squad, Jedi Master Secura has asked me to take my squad with you to where ever you are going." John thought to himself, "Somehow I knew Aayla would do something like that." John told Sargent Videc, "well Sargent, get you troopers on board, we're leaving now." Sargent Videc acknowledged and told his squad, "Alright Viper squad, let's move." The clones the got on the shuttle and John powered it up to take off towards Tython.

While in route to Tython, John contacted Aayla. When she answered, John said, "I received the squad of Clones you sent to accompany me." Aayla looked confused and said, "I never sent you a squad of clones." John then said, "Then why did…" John got interrupted by a voice saying, "Hand's up." John looked behind him to see the clones of Viper Squad pointing their blasters at him. John then said, "I'll… call you back Aayla." John ended the transmission before Aayla could say anything. As John slowly stood up, he said, "So, who sent you to kill me?" Sargent Videc chuckled and shot a stun round at John, knocking him out.

When John woke up, he was in a holding cell. He searched for his lightsaber, he realized that it was gone. Just then, the door to his cell opened and Sargent Videc walked in with 2 B1 Battle droids behind him. John looked at Videc and before he could attack, one of the B1 Battle droids fired a stun round at John knocking him out again. When he awoke again, he was in a room that looked like an interrogation room. Like before, the door to the room opened and Clone Sargent Videc walked in with 2 B1 Battle droids and a woman with pale-ish looking skin and a bald head, she had two weird looking Lightsabers. Sargent Videc slapped John across the check and said, "You will now tell us what type of weapon is on Tython." John looked at Videc and chuckled. John then said, "Why would there be a weapon on Tython? Even if I knew there was a weapon on Tython, I wasn't going to Tython to get it, I was going there for a personal vendetta." The woman walked up and said, "My name is Asajj Ventress, and you will tell us what you know about the Republic's new weapon." John looked at Asajj and said, "I'm not sure you heard me tell the traitorous Clone here, but I do not know what you are talking about." But before Asajj or Sargent Videc could say anything else, an explosion from a different section of the ship they were on rocked the entire ship.

When Asajj stood, she took out a communicator and contacted the bridge. When the OOM command battle droid answered, Asajj said, "Report, what is going on?" the OOM command battle droid told Asajj, "A republic Cruiser jumped out of Hyperspace behind us and took out our hyperdrive when they took out our engines." John smirked at the report as Asajj and Sargent Videc grew angry. John then started to laugh at the Separatist's Predicament. When Sargent Videc asked John what was so funny, John told him, "I just find it hilarious that you didn't have a full fleet protecting this ship and that will be boarded so they can find and rescue me, but I intend to free myself." John then used the force to pull his Lightsaber from Videc's grasp and used it to cut power to the device holding him. After he freed himself, John cut down the two B1 Battle Droids as Asajj and Videc ran out of the room.

On the Republic cruiser Valiant, Anakin and Aayla stood on the bridge as the guns crippled the Separatist ship. Just then, Anakin received a message on his wrist communicator. When Anakin answered it, the caller said, "Anakin, its John." Anakin was happy to hear his friends voice and said, "John, where are you?" John told Anakin, "I'm on the separatist ship you're attacking and I'm making my way to the escape pods right now." Anakin nodded his head and said, "Understood, I'll send a shuttle out once we take care of the Separatist ship." John said, "Understood, I'll await pick up." John then made his way to the escape pods to use one.

After launching the escape pod John was in, he watched as the Munificent Frigate got destroyed by the Republic Cruiser. After he was picked up, Anakin and Aayla arrived in the hanger to help John out of the Escape Pod. When John did step out, Aayla pulled John into a hug, to which John was glad to return the hug. All Anakin did was cross his arms and smirk. Anakin sensed in both John and Aayla a feeling that he was all too familiar with, that feeling…was love. When John and Aayla parted from the hug, Anakin said, "Well, I know for a fact that you two are perfect for each other." Before Aayla could say anything, John said, "Well…" when Aayla and Anakin looked at John, he then said, "There's something I have been meaning to tell you Aayla. You see, over the past few missions we co-commanded, I began to sense something in you that I've only sensed once before, in my deceased wife." Aayla then realized what he was trying to say, and before he said anything, she cleared her throat and she said, "Well, if you're saying that you love me and are worried about the Jedi Code, don't worry, because I love you too." John smiled and before he could even say that he was happy, Aayla pulled John into a kiss, like the hug, John happily returned.

After making sure that John's first wife's Lightsabers were secured, John continued his journey to Tython, this time Aayla went with him. Anakin moved his fleet to temporarily take command of John's and Aayla's forces. After the T6 Shuttle exited Hyperspace over Tython, John plotted a course to where his deceased wife was buried. When the ship landed, John and Aayla walked out and made their way to the ancient Jedi Temple to where the Jedi housed in the days of the Old Republic. When the two Jedi got to the burying ground of the Jedi, they knelt to honor the Jedi that have fallen. When they stood up, they entered the grounds to find John's Deceased's wife's grave. When they found it, John fell to his knees, pulled out the box with his wife's Lightsabers in and placed the box on her grave and said, "I hope you rest in peace now, may the force be with you even in death." There was a moment of silence before the Jedi left the resting place and got on the Shuttle to head back to their fleets. Along the way, John and Aayla received a call from Master Windu and he said, "John, Aayla, the council knows that you two are lovers." Then John said, "Master Windu it was my fault, I pulled Aayla into a kiss after I told her my feelings, let her stay on the council and give her control of my legion; I am more than willing to return to Coruscant and be stripped of my rank."

"That will be discussed later, when you get to your fleets return to Coruscant, we have come under attack by the Separatists." Replied Windu. John said that they would be there as fast as they could. Mace then said, "Just get her quickly, may the force be with you." Mace then ended the call allowing John to say, "Looks like the war marches on." Aayla agreed with John as they landed on Aayla's flagship The Liberty III, so John could take his starfighter back to his flagship. Before he left the hanger, John looked at Aayla one more time and said, "See you at Coruscant." Aayla nodded her head and said, "If you die, I'll kill you." John chuckled and took off towards his flagship.