John Sheppard

2007
After Atlantis tried to escape Lantea from the Asuran Stargate satellite weapon, the beam grazed the tower and incapacitated Weir. When Atlantis was stranded in deep space with 24 hours of power left, he was appointed the commander in charge, and went with McKay, Ronon and Weir to Asuras to make the steal of ZPM and upload a program that would make the replicators attack the Wraith, but lost Weir in the process. His command was replaced by Colonel Samantha Carter. He was actually on the short list, but the command was given to Carter in the end. Sheppard didn't mind, as he said he never wanted the job.

Whilst he was on a routine resupply mission to an offworld base, his Jumper was disabled and was kidnapped by a race of people he would know as Travellers. They needed him to power a stranded Aurora-class battleship to help the race's population troubles. He sent the ship into hyperspace, but was later attacked by the Wraith. He worked with Larrin to deter the Wraith from the ship and was released when he proposed an alliance.

He encountered "Todd" again, who proposed an alliance when the Asurans were wiping out Human worlds to stop the Wraith. They worked in trying to shutdown the nanite base code. After McKay and his sister were kidnapped, he helped in breaking them out. However, nanites would attempt shut down Jeannie to heal her of her epilepsy. "Todd" was almost finished on a away to shut down the nanites until he collapsed and needed a Human to feed on. Sheppard turned to Henry Wallace, the kidnapper, who had lost his daughter due to the nanites. He convinced Wallace to sacrifice his own life in order to shut down the nanites.

2008
With the failed raid on Asuras, Sheppard was quickly thrust into a heated situation between the Travelers and Atlantis, along with over two thousand refugees still on Atlantis. He participated in a rescue mission to save Laura Cadman and her team from a Genii attack on the planet Larrus, both saving her team, and alienating the Genii from Atlantis. Sheppard heard that his father died of a heart attack, and came to attend his wake. It was there that he learnt that his father regretted the argument they once had that drove them apart. Too angry and stressed to care at this point, John broke his brother's jaw in a fit of rage and left his old home swearing never to return. He then handed Ava Dixon over to Major General Jack O'Neill in order to prevent the IOA from using the Human Made Replicator as leverage against a potential evacuation of Pegasus.

Having learned from Mila theTraveler and Dr Radek Zelenka of the Wormhole Drive, John came up with a plan to take over Atlantis with the help of the Travelers and take Atlantis to another galaxy to escape the Asurans and Wraith. He recruited Ronon Dex, Teyla Emmagen, Daniel Jackson, Larrin, as well as several other of the Atlantis staff to assist him, including Samantha Carter who reluctantly joined up.

He shared a "mind-meld" with an Ascended Rodney McKay as prove to him the level of pain his friend had endured, an d why he had to stay ascended. John had an emotional breakdown at this stage and found himself being consoled by Samantha Carter while on Proculus. The event forever changed John as both the memories and feelings of Dr McKay were transferred and he has trouble distinguishing between Rodney's and his own.

This plan was later carried out after retrieving several ZPMs stolen from Asuran Warships. The act of mutinying and having to stun and confine his former comrades was a difficult one and despite both being on the side of the coup, he hadmany arguments with Samantha Carter, eventually boiling down to an emotional fist fight. Samantha later regretted it, and with their relationship teetering between inappropirate and unheatthy,John felt shame at asking her for comfort.

Using the Asurans as a distraction, John then piloted Atlantis using the WormHole drive to sucessfully escape the Wraith who had been laying siege. Atlantis and all the refugees aboard. had arrived inthe Hoag's Object Galaxy, a galaxy which Atlantis's database mentioned as having been explored by the Ancients.

Hoag's Object
Once in Hoag's Object, John Sheppard mostly stuck around the former Atlantis Expedition members. He developed a friendship with several Travelers including Nevas, Katana, Reyna, among others whom he'd begun to coach and train, as well as taking Alicia Vega under his wing to prepare her for taking over Major Lorne's duties.

Two weeks after arriving in the galaxy, he was among the medics who took Carson Beckett out of stasis and later was with teh Doctor as they explored the mainland of the moon they'd landed on. He was especially distraught over the Doctor's position and felt personally responsible. The Doctor also accurately guessed that John and Samantha were avoiding each other outof awkwardness from thier last few nights in Pegasus.

On the mission to the mainland, he found himself at odds with Alicia Vega who was acting out for an unknown reason. He quickly took control of the situation despite some hesitation, and in the end Vega respected his command.

While exploring the ancient ruins, Sheppard and Vega were attacked by an unknown entity which while appearing relatively humanoid, was difficult to focus on. The entity attacked them both and left Vega with a concussion and Sheppard with a bruised posterior and pride, before leaving using the Hoag's Object Stargate Network. John continued his role as military ocmmander despite not having a military, and soon developed a camaraderie with Vega

A few weeks after the incident, Sheppard and his team investigated a destroyed refugee village, It was found that the Refugees were still fighting amongst themselves and Atlantis could do little to stop it.

When contact with the Traveler ship Hylea was lost, he escorted Larrin alongside a large recovery team to the planet where the Hylea was. This was Atlantis's first encounter with "The Shade" though they didn't know it at the time. They barely escaped and soon, the planet and Hylea were completely destroyed despite being able to rescue the Travelers who'd been stranded.

He participated in the rescue of Rafaela Esposito from a deranged Sylek, using an AT-4 Rocket Launcher to destroy a Shade Gremlin.

Later, he along with Ronon Dex and a support team engaged Olim Primus Locagos Aquilina Centaurus to rescue Laura Cadman and Alicia Vega. Only through sheer luck did they survive, and all were moderately injured.

Invited to the Olim colony of Magna Secundus, John was one of the only ones to be treated with any respect by the Olim, He deferred that respect to Samantha Carter and Daniel Jackson, and was quite annoyed with the Olim's racism.

When the Shade invaded the planet, he fought alongside the Olim and his team to help as many people evacuate as possible, despite their success, Samantha Carter and several Olim Soldiers were left behind wounded. John took the risk of using the untested Alcaeus Armor they had stolen from Aquilina Centaurus and used it to rescue Samantha Carter with some timely assistance from Alicia Vega and her team.

Taking a less active role in off-world missions, John began to dedicate his time to training Travelers in Earth militayr tactics. He developed a friendship with Nevas, and soon the Traveler security force gladly aquiesced to his command.

2009
During Christmas, he participated in Chuck's party and gifted his "Fry" figurine to Samantha Carter, as well as giving his friend Alicia Vega the gag gift of a red bikini. HE was quite surprised to have gotten Sam's "Leela" figurine as a gift back proving just how like-minded they could be.

He was injured on a recon mission with Alicia Vega and Dusty Mehra shortly after Christmas, the event was a revealing one to Alicia, but soon her rationalizations retook hold.

He assisted Samantha Carter in retrofitting an F-302 Starfighter with Traveler Technology, they've named it the "Razor" modification.

Using his newfound 'Spidey' sense, John was able to detect and ambush an Olim Ambush party during the Olim Invasion of Atlantis.

Relationships
Prior to coming to Atlantis, John's ability to form meaningful relationships with others was poor; he and his father hadn't spoken with each other for several years, and his marriage had fallen apart due to his inability to be there for her. However, since arriving in Atlantis, he has formed close bonds with several people, ranging from the senior staff to offworld allies.

Atlantis Team
Easily the closest bonds John has formed since coming to Pegasus are the bonds he shares with his teammates on AR-1. Although he and Doctor McKay are prone to the occasional argument, with McKay sometimes growing frustrated with John's apparent assumption that he can automatically save the day when scientific problems arise. The two have shown on many occasions that they have both a great esteem for the other's abilities and share a surprisingly close bond, with McKay commonly attempting to help John when he suffers from personal problems despite his own poor abilities with relationships, such as when he attempted to express his sympathies following the death of John's father. The two have also been shown to spend a surprising amount of their leisure time together, both of them playing what they initially believed to be a Sims-like game before learning that it was an Ancient experiment with real people.

With Rodney McKay's apparant death in the raid on Asuras, John quickly becomes depressed. He relies heavily on Ronon and Teyla for solace, and finds a surprising friend in Samantha Carter.

Rodney was eventually found to have survived the Asuran's during a recon mission to Proculus, it was then revealed to John that Rodney had been tortured beyond the realm of his understanding, and had to ascend in order to find peace. Before leaving, Rodney shared a "mind-meld" with John to prove to him that the level of pain and angst he suffered was too much to live with.

The 'mind-meld' had an unfortunate side-effect of giving John the buried memories and feelings of Doctor McKay. This complicated life severely for John, but both men understood that it was the only way forJohn to understand. On several occasions, John has been unable to differentiate his own thoughts and feelings from McKay's. This led to an awkward bond between Sheppard and Carter given McKay's feelings for her, as well as Sheppard's own growing feelings for Carter.

The most obvious bond he has formed on his team is his friendship with Ronon, which has been compared by many to the bond between Jack O'Neill and Teal'c Both featuring human military leaders forming close bonds of respect and loyalty with alien soldiers who obey the other out of respect rather than adherence to the chain of command. The two men have been seen as having an almost brotherly relationship, Ronon leading the search for John when he was captured by Commander Kolya and later regretting not accompanying Sheppard back to Earth for his father's funeral. His friendship with Teyla Emmagan is another example of his ability to bond with others despite different backgrounds, believing in Teyla even when evidence suggested that she was feeding information to the Wraith--both deliberately and unintentionally--and showing great concern for her during her pregnancy. Teyla considered naming her son after him, but given the events of the last 6 months in Pegasus, chose to name him after Dr. Rodney Mckay

At one point he admitted that he didn't really have a family and his team and Weir were the closest thing he had to one.

Elizabeth Weir
Although she initially only recruited Sheppard for his powerful ATA gene, Elizabeth Weir came to greately respect John's abilities as a soldier, particularly after he single-handedly saved Atlantis from a Genii invasion. When Colonel Dillon Everett arrived to take command of Atlantis following Earth's discovery of a new Zero Point Module and the news of the approaching Wraith Hive-ships, it was John who convinced Everett to keep Elizabeth in the loop if he wanted to maintain the support of the rest of the city. Elizabeth reciprocated this respect by insisting that John be promoted to Lieutenant Colonel rather than allow someone else to take command of Atlantis after the expedition regained contact with Earth. Elizabeth continued to visit John even after he began to mutate into a Wraith-like creature following his confrontation with Ellia and the mutated Iratus bug retrovirus, John reciprocating this compassion by risking his life to try and urge her to keep fighting after she was infected by Asuran nanites during her enounter with Niam. John was clearly deeply affected by Elizabeth's loss when he was forced to leave her behind on the Asuran homeworld, and his grief when he learned that she was dead--having first heard a second-hand account from the Organic Asuran duplicates of his team and subsequently witnessing Rodney McKay's memories of her sacrifice to save McKay from the Asurans. Given Elizabeth's last message to him, he finally realized that his feelings towards her were reciprocated.

Before Asuras
A friendship born of necessity, Larrin originally wanted Sheppard for his ATA Gene to learn how to mimic the gene for non-gene carriers. She kidnapped him and forced him to assist her and her people in recovering an old Lantean Aurora Warship. They immediately showed attraction to one another, but given the situation at the time, neither felt more than a physical attraction.

Working together, they suceeded in destroying a Wraith Hive, securing the Aurora for the Travelers who had dire need for the space it would afford them. Larrin eventually let Sheppard go after some convincing that they were better allies than enemies.

Asuras
A few months later, Larrin agreed to offer her support in the raid on Asuras. She had Sheppard come to the Aurora in order to pilot it during the battle, and suceeded in destroying several Asuran Auroras in the surprise attack. Several other Traveler Generational Ships joined in the assault.

The battle was a catastrophe for the Travelers, Once Fran was disabled, The Asurans regrouped and quickly destroyed a pair of Generational Ships and damaged the Aurora. Larrin fled the area with her remaining ships, kidnapping Sheppard once more. Several weeks passed, with Larrin torturing Sheppard out of anger and spite. Eventually, she came to understand that Atlantis was the only hope the Travelers had now that the Asurans were nigh-unstoppable

While there, she confronted Sheppard many times about a potential relationship and whether he would act on their mutual attraction or not. It was primarily a ploy to keep Sheppard on his toes around her, but eventually she did come to realize that she might come to have real feelings for him.

The "Plan"
After the Midway Disaster, Larrin was prepared to flee Atlantis and try and hide from the Asurans and Wraith. She was willing to bring Sheppard along as a pilot for their Aurora, and offered Sheppard the position. When he countered with his own plan, Larrin was torn. Seeing the potential in his plan though, She convinced the Traveler Council to remain on Atlantis and assist in securing more Zero Point Modules.

Despite her growing feelings towards Sheppard, she had quickly formed a friendship with Chuck Campbell who had been training her in Atlantis's systems. As per the "Plan", Larrin prepared her security force to take Atlantis by force. The plan was prematurely set into motion though when Richard Woolsey arrived with an offer from the IOA. Larrin rejected it out of hand, and eventually had a brief but enlightening talk with Sheppard. He told her that he wouldn't be leaving Atlantis anytime soon, not even for her. With this knowledge, Larirn forgot about the potential relationship and focused on Atlantis eventually starting a platonic sexual relationship with Chuck Campbell.

Despite their rocky romantic relationship, John still trusted Larrin enough to give her control of the Coup, as well as with the knowledge of his "mind-meld" with Rodney.

Hoag's Object
Larrin began to grow resentful of the supposed happiness of the "Earthers" in the new galaxy, and often bickered with John and the others. Eventually she broke off her relationship with Chuck, and was the only one to know of John's depression over Samantha Carter's 'Mornin' Jack' incident.

After Contact with the Olim.
With Samantha in stasis on the verge of death, Larrin found herself going to John again. Ashamed and emotional, she silently begged John for comfort. Too tired and exhausted from the earlier battle and negotiations, they simply spent the night together in order to sleep.

The next day Larrin entrusted John with teh secret that she had never loved anyone, because she was afraid that people she loved would die and she didn't think she could take that.

A few weeks later, seeing John and Sam getting closer together, she forcefully tried to reheat their never started relationship by going to John's office and forcing herself on him.

Afterwards, when she tried to expand it to an actual relationship, she and John came to blows and have been on the rocks ever since.

Alicia Vega
One of the more unusual relationship's he's had is with Alicia Vega, one of the renegades to come with Atlantis to Hoag's Object. Their relationship has gone from Alicia showing attitude and general discontentment, to thinking that they'd have a great relationship. With Ronon on the mainland and with Dusty, John has found a new friend in Alicia, and despite her affections for him, he's not reciprocated because while he does care about her, she knows next to nothing about him.

Alicia has asked Sheppard about thier potential relationship, and while she always admits that they've become great friends, whenever it becomes something 'more', John is adamant that the chances of such a thing are insignificant.

John considers Alicia to be almost like his sister in some respects, trusting her as his second in command and the new leader of AR-1.

Before Asuras
Easily his most unstable relationsihip, John has come to trust Samantha with his life and well being. John originally met Samantha during his briefing at the SGC prior to going to Atlantis. They never really thought much of each other given their completely seperate lines of work.

John had heard many stories about her though from Rodney McKay, and when he finally got to know her on her visit to Atlantis aboard Odyseey, a fast friendship was born. Samantha was especially pleased to learn that despite Rodney's changing habits, Sheppard still carried a lemon around with him.

When Elizabeth Weir was lost to the Asurans, John was quite glad that Samantha Carter was chosen as the new leader of the expedition, himself not wanting it and glad a like-minded individual had taken the reins. They often spoke on the balcony outside the gate room about the issues surrounding hte city, sometimes even just about how thier days were going and the difference to the SGC.

Despite frustration that she wouldn't allow him to go and try and rescue Elizabeth Weir, John still appreciated her friendship enough to invite her for a beer after Ronon's "return" after the events of "Reunion" in a deleted scene in Season 4.

Their friendship and camaraderie continued well into the year, despite several dark setbacks with the Asurans and Wraith.

Battle of Asuras and aftermath
When Sheppard was kidnapped a second time by Larrin after the failed raid on Asuras, Samantha grieved and worried about him (Reference: Tainted Treasure, Isolation)

Samantha was also the one to take the responsibility of telling John that Rodney McKay had been listed as KIA. She grieved with him in solitude on the Balcony outside the gateroom before being interuppted by Captain Cadman's plea for help from the planet Larrus. Given the circumstances, she agreed to let John lead a team to rescue the endangered Captain.

Pariahs
A few weeks after the incident with teh Genii on Larrus, Samantha Carter was recalled for a briefing with the IOA alongside Sheppard. In another tragic moment, Samantha was also the one to tell John about his father's passing.

By this point, both leaders had grown to respect each other completely, and often would joke around in order to lighten the mood.

While on Earth, Samantha felt sympathy for John having just lost his father and decided to accompany him to the wake seeing as Ronon could not come with him given the growing crisis on Atlantis with the refugees. She began to get to know John as she saw and learned how Sheppard grew up. Quickly their friendship blossomed despite the hard moments they were both going through.

At this point, John trusted Sam enough to tell her a little more about why he was estranged with his family and even explained his violent outburst towards his brother Dave.

Before leaving Earth, Samantha was quite surprised when John asked her to accompany him to a Carnival on a "date" seeing as it might be their last night on earth. Hesistant at firs,t Samantha decided to give him the benefit of the doubt and agreed. It would be a night she would not soon forget.

With John having donated the majority of his inheritance to the IOA relief fund, Samantha was quite confused with John's impulsive nature during their date. See Article for details.

Now much closer friends, they worked almost seamlessly well together and showed obvious care for each other. Both Jennifer Keller and Daniel Jackson noticed the obvious friendship blossoming. They would often play chess and have lunch together in order to discuss the goings on in Atlantis and how they were going to maintain a level of order.

When John was injured in the Genii mining facility. Samantha took Daniel along with a rapid response medical team to rescue both him and Jennifer Keller. She began to admit to herself that maybe she cared a little too much for him, and decided to not push any further after Larrin accused her of having feelings for him.

After the Midway disaster in which Daniel Jackson and Ronon Dex were left stranded between galaxies, and confirmation that the Wraith knew where Atlantis was, Samantha worked herself ragged trying to figure out a solution.

John found her passed out on her desk and his obvious care showed through his demands that she get some sleep. Samantha began to crack around the edges when she asked John to have a few drinks with her on one of the piers. While there, Samantha quickly got drunk in an effort to loosen up enough to talk without inhibitions.

John became worried, but understood where she was coming from. Samantha admitted she was more worried about Daniel than she was about the city, and John assured her it was just natural and he knew she wouldn't abandon the city. Samantha then dropped the bombshell that she knew John was planning something and he'd better tell her beforeshe found out on her own. Despite playing dumb, Samantha easily torehis defense apart and John confessed to the plan to stage a coup.

Torn between her loyalty to Earth and the USAF, as well as her moral obligation to save Atlantis and those on it, Samantha agreed to reserve judgement in the hopes of a better plan.

Their bond was undeniable at this point, and they shared a hug before parting ways that night (With a rather comical freudian slip.)

Their bond undeniable, their friendship suffered nonetheless. No longer did they play chess or share meals, it was all strictly professional unless they argued. Once the upgraded Daedalus arrrived from Earth, Samantha was let in on the full plan alongside the other renegades.

Constant arguments with John continued despite finding out even more about each other, including the common trait of both having 'shared' themselves with ascended beings. While on Proculus to ask Chaya Sar if they could hide refugees there, they both encountered an ascended Rodney McKay who shared a "mind-meld" with John. Samantha watched as Sheppard had an emotional breakdown and Rodney finally ascended beyond this plain of existance. Rodney's last words to her were to take care of John.

Grief stricken, Sam stayed by Sheppard's side, consoling him and sharing some of her darkest secrets to help him cope with the pain Rodney had shown him. It was by far one of the most bonding moment between the two as Samantha saw Sheppard in his most vulnerable state.

When they returned to Atlantis, things quickly fell apart, and Samantha was left with the hard decision of exposing Sheppard and his coup, or going rogue and assisting him. Given all her experiences in Atlantis and refusal to abandon the Pegasus Refugees to a doomed fate, Samantha reluctantly joined the Coup alongside John.

The coup and awkward comfort
Mostly arguing about the situation, Samantha called on Sheppard to assist her in rescuing an injured Doctor Jackson. After a bloody struggle resutling in dozens of injuries, the coup was finally over.

Frustrated to the breaking point, Samantha finally dialed Earth and spoke to Jack O'Neill about their missed potential relationship. Finally breaking her control. Sam locked herself in her office to have her private emotional moment. John found her there and after some convincing, consoled her in her fragile state. They both understood that the intensity of the last few days had taken their toll and they needed each other's support to keep going.

Accompanying her to visit Doctor Jackson in the infirmary, Sam showed much stronger animosity towards John, but was too tired to fight his offer to walk her to her quarters. Feeling the need to offer her a way out, John admitted that he wouldn't be angry or dissapointed if she chose to head back to Earth. Their talk quickly boiled into an argument, leading to Samantha slapping John hard across the face. John didn't fight back thinking that he deserved it.

In the adrenaline fueled moment, Samantha let her repressions out and proceeded to beat the crap out of John right outside her quarters. John hardly fought back, almost laughing at the rightousness of the moment. Samantha nearly killed him right there, but stopped as the emotional impact of what she was doing hit her.

Dragging him into her room, she used a Tok'ra healing device to patch John up. Both emotionally drained and vulnerable, they both admitted that the situation was breaking them. A simple hug turned into a full embrace on the bed. Recovering though, both of them pushed away and realized just how much the coup and situation had drained them. Both finally agreed to simply wait, to leave "that" until they had time to work it out, if they had time. They spent the night together and found it to be quite awkward the next day.

Despite all the problems they were having with the coup and the awkwardness of their relationship, they still promised to support each other, and when John had a moment of weakness upon seeing Oberoth, Samantha was torn between helping him and carrying out their plan. Later thatnight after spearking with all the renegades, Samantha went to John's quarters to see how he was coping. John begged her to stay with him and she reluctantly agreed as long as they kept it platonic.

In th emorning, they both admitted to having feelings for one another but to be unsure of what that meant. John was unsure if the feelings were his or Rodney's, and Samantha was still grieving over the fact that she was leaving Earth behind. Eventually they decide to wait till Atlantis was safe before trying to decode this issue.

During the final battle, Samantha stayed by Sheppard's side during hte transit through the wormhole diive.

Once landed on the yet unnamed moon, Samantha and John finally agreed that they needed time alone before working out their differences. They began life in Hoag's Object on relatively uneasy terms.

Hoag's Object
A little over 2 weeks passed with relative discomfort. Everyone was noticing John and Samantha were avoiding each other and having problems. Sheppard would talk with Teyla and Ronon, while Samantha confided in her best friend Daniel Jackson. At this point, exploration of the galaxy had just commenced to search for habitable planets to scavange for food and settleable areas.

Samantha decided that despite neither of them being in a good position, they needed to support each other in this grieving time. She again went to his quarters and after some awkward TV watching, they agreed to support each other to their limits.

Unhealthy Relationship and "Mornin' Jack"
They began what could be deemed a relationship in the sense that they were spending time together. A few times a week, they would get together and watch old Earth Cartoons and chat. Usually they spent those nights together to feel some degree of comfort. Their friendship quickly returned, but any hinting of romantic feeling quickly turned the situation awkward.

It continued for almost two months, when one morning after a Futurama marathon, Samantha woke up and accidentally called John "Jack". John said nothing, but Samantha quickly caught her error and their relationship broke at that instant. Their friendship suffered greatly as well, though both still admited they cared about each other. John would often worry about Samanths's well being, and Samanthe would watch from afar as John continued to try and encourage the people who'd come with them... including Alicia Vega.

Contact with the Olim
By the point at which Atlantis encountered the Olim, Samantha and Sheppard were still uneasy around each other, but they'd worked out their professional differences... mostly.

When the Olim were condescending and racist towards Samantha for her lack of the ATA gene and general unevolvedness compared to even Sheppard, John showed an intense protective nature of her. Samanthat quickly chided him that she could take care of herself and their entire friendship was put on edge.

During the Shade Invasion of Magna Secundus, they repeatedly butted heads over Samantha's decisions and safety. Samantha would later realize that she was taking her position too seriously and John's protective nature wasn't over their feelings, but rather he was truly worried about her safety.

When Samantha was trapped in the Olim Subbasement after the initial attack, John Sheppard used the stolen Alcaeus Armor from Aquilina Centaurus to survive the harsh conditions of the soon to be destroyed planet to search for her. His determination paid off when he found her near death and frozen in front of the Olim HQ, quickly taking her back to Atlantis thanks to the timely assistance of Alicia Vega, Dan Drake, Dusty Mehra and Ronon Dex.

Several days passed as Carson labored to save Samantha's life. John shutting out all his emotions except for a moment with Larrin where he admited that he had loved Elizabeth Weir, and another with Daniel Jackson in front of Samantha's stasis pod where he admitted that just like Samantha couldn't lose Daniel, John couldn't lose Samantha.

When Samantha began to recover thanks to Carson's tireless work, She and John had a small heartfelt conversation where they finally resolved their issues - They didn't love each other, but they thought they could.

The next few months were much more stable and their friendship quickly healed, despite some rocky moments like Larrin's instictual reaction, and Samantha's stubborness to refuse help in recovery, within 4 months they had began a new relationship.

Approximately 300 days from teh time they arrived in Hoag's Object, they finally consummated their relationship on the mainland of "Saudade" after a day of relaxation. Their glee was short lived however, as the Olim Invasion of Atlantis quickly put all their thoughts of a relationship on hold.

Family
Sheppard is estranged from his family. He had a wife, but they divorced after she couldn't take all of the secrets, despite encountering each other once more when John came to Earth to have a briefing with the IOA, they were never able to reconcile their differences. His father and brother were businessmen and his father wanted him to be one too and they had a falling out when he wanted to join the Air Force. Sheppard felt he wasn't welcome by them afterwards and seemed to think he had no family as a result. He did return for his father's funeral and his brother thought he only wanted money from their father's will after being gone so long. John furthered the rift between his family at the accusation by breaking Dave's jaw with an angered punch. His brother, Dave, revealed to him that his father always regretted their fight and wanted to make up but never got the chance, which John ignored in a fit of rage. John spent his last night on Earth away from his family, instead going to a carnival with Samantha Carter.