After getting to know his Clone troopers better, John posted to the Galactic Web an ad to become his Second-in-Command. The next day, John saw that only 1 person showed up, the person was a female Tortuga. He was disappointed, he thought that more would come. John decided to take the only person that came and make her his Second-in-Command. When John asked the person what her name was, she said, "My name is Sotta Kilaa, and I thank you for giving me a chance to prove myself to be worthy of your Second-in-Command." John nodded his head and said, "You are most welcome Lieutenant Kilaa. Come, the shuttle to our forces is just up ahead." As John and his new Second-in-Command made their way to the awaiting LAAT, John asked Sotta, "What do you have regarding combat?" Sotta looked at John and said, "I have an IQ of 200." John stopped in his tracks, looked at Sotta and said, "You have an IQ of what?" Sotta repeated herself by saying that she had an IQ of 200, John was surprised to hear that and he said, "So you can create great strategies?" Sotta nodded her as she got on the transport and then she said, "I can also predict what an enemies next move is before they even give the command." John was impressed and said, "Well Sotta, I think we can get along just fine." Sotta smiled and agreed with John as the Transport exited Coruscant's Atmosphere and made its way to the Jedi Cruiser named after John's first ship, The Bravery.

When the shuttle landed in the Hanger Bay, John and Sotta stepped of it to be greeted by Captain Baccara. Captain Baccara saluted the two and said, "Welcome on board General, and I take it that this Tortuga is your Second-in-Command." John nodded his head and introduced the two. John said, "Captain Baccara, this is Lieutenant Kilaa. Lieutenant Kilaa, this is Captain Baccara, he was supposed to be my Second-in-Command, but the Jedi Council gave me permission to choose a Non-Clone Republic Citizen to be my Second-in-Command." Captain Baccara and Lieutenant Kilaa shook hands and Baccara said, "General, we have our first mission. Its ready to view at your disclosure on the Holo-table on the bridge." John nodded his head and asked both Captain Baccara and Lieutenant Kilaa to accompany him.

A little while later, on the bridge, John, Sotta, and Captain Baccara exited the elevator. To John's surprise, Aayla Secura was at the Holo-Table. "Hello Aayla, what are you doing here?" John asked his fellow Jedi Master. Aayla told John that she would help him on his first Mission, by order of the council. John smiled and asked, "Where are we being sent?" Aayla brought up a planet and she said, "This is the Planet of Taris." John's attention intensified when he heard the name of the planet, he remembered it from when he landed on the planet to help deal with the Rakghoul Plague, he wondered if there were still Rakghouls left on the Planet. John's thoughts were interrupted by Aayla saying, "John, did you hear all that?" John looked at Aayla and said, "Huh, sorry I was in deep thought." "What were you in deep thought about?" Aayla asked with curiosity in her voice. John replied to Aayla's question by saying, "The Planet Taris, I was there before, back when the Republic tried to resettle the planet, there were creatures called Rakghouls, they were Republic Citizens, troopers, and Imperial troopers that were infected by a disease created by a Sith Lord that went by the name of Karness Muur. Muur was seeking a way to become immortal and achieve Galactic Conquest, so he created an Amulet called the Muur Talisman."

John then told his comrades that only those who are Force-sensitive and beings belonging to Certain Species are immune and will not be changed by the talisman's power. John then said, "However, if someone was scratched or bitten by a Rakghoul that person WILL turn, even if that person can use the force. When I landed on the planet, I was tasked to hunt down a rouge Jedi and bring him to the Council for questioning. I eventually did find him, but he was bitten by a Rakghoul and was weak. I got him to the Temple before he became one of them and we had him in a cell to see if we could create a permanent cure to the Rakghoul Plague." Aayla then asked John if the council created the cure for the Rakghoul Plague, to which John replied, "I don't know, I was assigned to the Taskforce, the one I told you about in the Temple, before I could find out if they made a permanent cure." John then got the conversation onto the Mission.

Captain Baccara reached into his pocket and pulled out a Holo-disk and stuck it into the Holo-table. The Planet of Taris came up with Separatist ships in a basic Blockade formation, and Republic ships just sitting in the spots they were in. But something was off, the ships looked like they were abandoned. Captain Baccara then said, "A few days ago, a small Republic freighter jumped into Taris space and saw the Separatists ships and made a hasty retreat and reported it to the Republic. A small fleet of ships was sent in, but we lost contact with them, as you can see, they haven't responded to any of our transmissions." John looked at the ships and said, "Prepare all ships to make the jump into Hyperspace, we're heading to Taris." Captain Baccara nodded his head before he went to tell the other ships in John's fleet to make the jump into Hyperspace.

Meanwhile, on the Republic Jedi Cruiser Defender, three clone troopers were running down a corridor while trying to escape creatures that were once their comrades. One trooper tried to hold off the creatures so his fellow troopers can get back to a room the clones barricaded to keep them safe, but that clone only managed to take a few of the creatures out before his spot was over run and he was dragged away. But the two other troopers got to safety of their 'Safe room' where other troopers were held up. The trooper who looked like a Clone Commander walked up to the two troopers and asked, "What happened, and where are CT-6538 and CT-6539?" One clone trooper, CT-6540, nicknamed Ducky, stood at attention and said, "Sir, the mission to get supplies was a success, but at the cost of CT-6538 and CT-6539 lives, they sacrificed their lives so we can get back here with the supplies to fix the Holo-table."

Back with John and Aayla's ships, they were in route to Taris. John was in his new quarters, he sat on his bed looking at a picture of his old team and his wife. John made a small smile on his face. His focus was interrupted when Aayla knocked on the door of his quarters. When John looked up and saw Aayla, he said, "Sorry, I guess I didn't hear you come in, what's up Aayla?" Aayla took a few steps in and said, "We'll be exiting Hyperspace soon, who are they?" John looked at the picture he had in his hand and motioned Aayla to sit down next to him. When she did, John told her, "This was my team and my wife, before we got married. We had this picture taken after we helped pushed Imperial Forces off Naboo. Back then was a different time, we didn't have any clone troopers and we had to face a couple hundred Sith lords in the entire enemy Army." Aayla placed her hand on John's shoulder and said, "I bet they were proud to know you." John look at his Jedi comrade and said, "They were actually, especially my wife, the Battle of Naboo was actually the mission that my wife and I started to take missions together and our feelings for each other began to blossom." Aayla smiled and asked John to look if she could look at the picture. John said, "Sure," and he handed the picture to Aayla. When Aayla got a good look at John's wife, she said, "Your wife looks very beautiful." John smiled and said that his wife was very beautiful. John then said, "You've should've met her in person, I bet you two would have gotten well together. She managed to make any angry creature calm down with her ability to use the Force to connect to creatures and find out what had the creature upset." Before Aayla could say something, Captain Baccara entered the door and said, "Generals, we're about to exit Hyperspace." John stood up and said, "Thank you Baccara, prepare a shuttle and get a squad of clone troopers." Baccara acknowledged John and left to follow his orders.

After Baccara was gone, Aayla stood up and asked John, "Why did you want him to get a shuttle ready?" John looked at Aayla and said, "I have a theory about why we lost contact with the fleet sent here before us, but I need to go aboard to confirm my suspicions." Aayla was going to ask who would he put in charge, but John answered her question by saying, "While I'm gone, I am giving command of my ships temporarily to you until my return." Aayla nodded her head and as John was walking towards the door she said, "May the Force be with you John." John turned to look at Aayla and said, "And You Aayla." John then exited his room to head to the Hanger.

A little while later in the hanger, John walked up to the transport he was going to use and saw the clones that were going to help him, but he didn't recognize the markings on four of the clone troopers Armor. One of the troopers that he did not recognize saw John, walked up to him and said, "General, my designated Number is RC-7278, but you may call me Sarge." John was confused by Sarge's clone number and asked, "Why isn't your clone number the same as the other clones?" Sarge told John that he was a Republic Commando, along with the rest of his squad, RC-7279, nicknamed Bullseye. Bullseye was the sniper of the group. Next to Bullseye was RC-7280, nicknamed Trenchman, he was the heavy weapons expert of Sarge's team, and finally there was RC-7281, nicknamed Hatchet, the Squad's medic. Sarge then said, "My squad and I have been tasked to follow your order and be a part of the 314th legion." John asked Sarge what he should call him and his team and Sarge said, "We're called Epsilon Squad." John said alright and he and the squad of clones, including Epsilon squad, got on the Nu-class attack shuttle and it took off to land in the command ship of the small fleet.

As the Nu-class attack shuttle made its way to the Derelict Jedi Cruiser, John told the clones what happened on the planet back in the days of the old Republic and their mission. John said, "We are doing some recon, the command ship that we're going to be landing inside is the Jedi Cruiser called the Defender. It's crew, along with the rest of the ships in the small fleet, have been out of contact for days. That's where we come in. the mission is simple, get in, get to the bridge, find out what happened, and get out. Does everyone understand the mission?" all the clones said, "Sir, yes sir." John smiled and said, "good, now lock and load." As the clones made sure that they were ready, the Nu-class attack shuttle made it into the Jedi Cruiser's Hanger bay and touched down.

When John stepped out of the shuttle, John said to Sarge, "Take you men to engineering, if you see anything that's not a Clone or a Jedi, shoot to kill." Sarge nodded his head and said, "Alright team, let's move." John then told the remaining clones, "The rest of you are with me, we head to the bridge." The clones nodded their heads and got their gear together. But John stopped two clones and said, "You two are to stay here and make sure that the shuttle is ready for takeoff." The two clones nodded their head and said, "Yes sir." John then turned to the other clones and said, "Let's go." John and the clones then made their way to the bridge.

Back on John's ship The Bravery, Aayla was watching the fleet when Commander Bly, her Second-in-Command, walked up to her and said, "General, we're receiving a message from The Defender." Aayla acknowledged the Clone and walked over to the Holo-table and answered the message by saying, "This is Jedi Master Aayla Secura of the Jedi Order, to whom am I speaking?" Suddenly, a clone popped up, and said, "Thank the force, we've been trying to reach someone in the republic." Aayla then asked the Mysterious clone to identify himself, the clone then said, "Sorry about that General. My designated clone number is CC-43656, but I prefer to be called Commander Flex." Aayla then asked Commander Flex about what happened with the fleet, to which flex replied, "After we exited Hyperspace, we saw the Separatist fleet and began to move into battle formation, but the commander in charge didn't have us engage because the Separatist ships weren't showing any signs of Power on any of their systems, so the commander sent a small team to investigate and we lost contact with them, so the commander sent myself and a squad of clone troopers over to find the troopers that were sent in before us. What we found on board was gruesome, helmets and clone Armor looked like it they were torn off the clone troopers. Bodies of some form of creatures littered the hanger floor. As we were about to disembark from the shuttle, 2 clone troopers came running out from behind a damaged LAAT. One of the clones was holding his arm and I saw that his arm had scratch marks, so I ordered the men that were near me to lay down covering fire for the two troopers as they made their way towards the shuttle. My men did as they were told and laid down covering fire. The uninjured clone trooper looked back and tripped over a chest plate, and before he could get up, the creatures that were chasing him and the injured trooper got to him and dragged him off."

Commander Flex then said, "The injured trooper got on the shuttle and I told the pilots to get us out of the Separatist's ship before those things got on board and they managed to do so. When we landed back on the ship, we rushed the injured trooper to the infirmary. But by the time we arrived, the trooper transformed in one of those things we found on the Separatist command ship and attacked one of the doctors. This "plague" spread throughout the ship, and the commander ordered all crew members to abandon the ship. Several of our boys used the escape pods and the other ships picked them up. As we boarded up a room we're using right now, we were receiving messages from the rest of the fleet, the creatures somehow managed to infect some of the men in the escape pods, which in turn infected the rest of the ships. We've tried to get in contact with the republic to quarantine Taris, but the holo-table we're using could only receive messages so we couldn't warn you."

Aayla looked at Commander Bly and said, "Get me Master John." Commander Bly nodded his head and attempted to contact John. Aayla looked back at Commander Flex and she said, "Commander Flex, we have a team on board the ship trying to figure out what happened, but we will tell them what you told us, or do you want to tell us your location so we can tell our team where to head." Commander Flex looked worried and said, "No, you have to call them back to your ships and destroy every ship in the fleet." Meanwhile on the defender, Epsilon squad finally made it to engineering and began downloading the files. As the files were being downloaded, Sarge contacted John and said, "General, we made it to engineering and are downloading the files." John nodded his head and said, "Good, we're almost to the bridge, once the files are downloaded, head back to the shuttle and wait for us there." Sarge acknowledged his orders and he and John ended the conversation.

After a few minutes went by, Sarge got a call on his communicator. When he answered it, the person who contacted him was John and he sounded scared. John said, "Sarge, forget the files, just get your team back to the shuttle, NOW!" When Sarge asked John why, John told him, "Cause this ship is infested with Rakghouls." After hearing what John just told him, Sarge looked at his squad and said, "Pack it up, we're leaving, NOW! We got Rakghouls on board." As Sarge and his team got packing up, John and the troopers with him found the survivors and checked to make sure no one was scratched or bitten, any who were scratched or bitten were asked if they wanted John to kill them or stay behind and die on the ship when they blew it up. After all the troopers were check, they made a bee line to the hanger where the shuttle was waiting for them.

When John's team made it to the Hanger, the shuttle was being attack by Rakghoul. The two clones John ordered to stay behind were defending the shuttle, along with Epsilon squad. As John and the clones with him fought their way to the shuttle, Commander Flex was ambushed and dragged off, along with Ducky and CT-6541. When everyone was reunited, they made their way onto the shuttle, not before a Rakghoul bit John in the arm. After John killed the Rakghoul and close the shuttle doors, he told the Pilots, "Get us out of here." The head pilot said, "Yes sir." And managed to get the shuttle out of the Hanger.

Along the way back to the Bravery, Sarge saw that John got bit and had his pistol at the ready and approached John and said, "Sir, your arm." John looked at his arm and said, "Well, in the exact same spot as the last time." Sarge was shocked at what John said and asked, "What do you mean 'again'? Do you mean that you were bitten before?" John looked at Sarge and said, "Yes, but I never turned, so I guess that I am genetically immune to the Rakghoul Plaque." Sarge wasn't sure if his Commander would turn or not, but he placed his pistol back in its holster. John then got on his communicator and called Aayla. When she answered, John said, "Aayla, order the ships to destroy the infested Republic ships and Separatist ships." Aayla agreed and ordered all Batteries to begin firing, within minutes, John's and Aayla's ships destroyed the Infested Republic ship and moved on to the Separatist ships and ended the Rakghoul on board the ships.

Later, in the Bravery's Infirmary, John was getting his arm patched up from where the Rakghoul bit him on the arm. Aayla and Commander Bly were surprised that John didn't turn into a Rakghoul. John told the two that he was bitten before, but with the help of the force, he kept the infection from spreading and it died out, causing him to be completely immune to the plaque. After getting the all clear from the Medical Droid, John and Aayla reported the status of their mission to the council. After hearing what John and Aayla had said, Yoda smiled and said, "Well done. The rakghoul plaque, if let unchecked, been devastating to the republic could have." Master Windu then said, "This mission has shown us that you two can work together well. So, the council has decided to give you missions that you two can complete together, well done." John and Aayla looked at each other and back at the council. John was the first to say, "Thank you Master Windu, Master Yoda, we'll not disappoint you." Master Yoda then said, "Very well, with you may the force be. Hmmmmmm." The council then ended the conversation. A few moments later, John and Aayla received their new orders. Aayla looked at John and said, "SO, how does it feel to command troops again?" John looked at his fellow Master and said, "I'll be honest, after being on ice, I'm glad that I was reinstated." Aayla smiled and said, "I'm glad, now let's get to work." John smiled as well and agreed with Aayla as their ships made the jump into hyperspace to make their way to their next mission.