Well, it took me a long time to finish, but yesterday I finally did finish ME3 with what became my canon Shepard 
So, here is her story.
Name: Hannah Shepard
Gender: Female
Class: Adept
Background: Colonist/Ruthless
Personality: Distanced, keeps to herself, tries to not meddle too much with people’s personal affairs, unless either asked or when she feels strongly about it (this plays around the idea to only use persuasion options or interrupts when it fits her character too much to not take them). She's the mission first type that gets the job done no matter what. This has gotten her a reputation as a ruthless soldier, but generally she wants to keep innocent civilians safe. However, she does not hesitate if she sees them as a potential source that could jeopardize a mission.
Romance: Kaidan (ME1/ME2), James (ME3)
The events on Mindoir left Hannah Shepard traumatized and scarred her whole life. She had watched her mom and dad being slaughtered by batarians right before her eyes, and the few friends she had died that day.
One year later, when she was detected as a biotic, she made up her mind to put her abilities to use and join the ones that rescued her – the Alliance. After enlisting, she strived for the best results, pushing herself to the limit. The Alliance became her home, her life, her escape from the pain of her past. Despite tending to keep to herself and trying to not let other soldiers too close, she was still friendly with them.
But the events on Torfan pushed her even deeper into a life of solitude. In blind rage and driven by revenge she snapped and sent most of her unit to their deaths in order to deal with the batarians she encountered there.
She shut down afterwards, emotionally drained, building an impenetrable wall around her to keep people from hurt and to keep herself from hurt.
She knew continuing to serve would only work if she dealt with the fact that there could always be more death. When that happens she puts her feelings aside to focus on the task ahead, but remembers the fallen afterwards.
She has learned to hide her true emotions behind a mask of indifference early on and it’s important to her to appear as a strong and unbreakable woman in front of others. She only deals with her emotions when she’s alone.
Even in the present she can never forgive what the batarians had done to her.
In Mass Effect 1, she’s a loyal Alliance soldier to no end and dislikes politics and corruption.
She doesn’t trust most aliens because of her past and she only reluctantly lets Garrus join because he already investigates Saren. When Wrex approached her at the C-Sec elevator, trying to convince her twice to let him join, she let him on board as well because krogan are supposed to be tough fighters and could be useful cannon fodder. She also did not want Tali to join, but ultimately had no choice when Udina made her do it.
After having Garrus, Wrex, Tali and Liara on board she decided to at least find out how they tick, in order to be prepared for battle in the best way. She learns very early that Garrus and she share some views and is pleasantly surprised by his goals in trying to take Saren down and his reasons to join C-Sec.
She barely talks to Wrex as he seems very untalkative, but when Garrus mentioned the genophage at some point she asks Wrex more about it. While thinking it’s a sad thing, she also feels it is a necessary evil, seeing how krogan are usually very violent.
She’s afraid Tali might spy on the Normandy, but she soon sees that Tali is no threat.
Liara strikes her as innocent right away and she’s the first of the aliens that she wants to truly know more about. Despite Liara's fascination with Shepard, about which she is very careful, Hannah had taken a liking to Liara, on the path to a blossoming friendship towards the end.
She grew to like Ashley because of shared feelings on aliens and family.
During her talks with Kaidan she quickly finds herself interested in him, fully aware she lets her guard down. But she can’t resist, she’s lonely and she likes him a lot, even though they strongly disagree about aliens. She ends up spending the night with him before Ilos because she longs for some human contact, and stays with him until they're separated when the Normandy is shot down by the Collector ship.
She brings Ashley and Liara to Noveria, because she thinks Liara can help when dealing with her mother. When they kill Benezia, Shepard feels guilty, she never wanted anyone to see their parent die, it hit very close to home.
Upon encountering the rachni queen, Hannah has no second thoughts about her fate. She kills anything that sounds dangerous to her, and she did not trust a word the queen said.
She agrees to use the nerve gas on the colonists, but this changes when she sees how close the Thorian Creepers have gotten to the colony. She fears the colonists share the same fate and she doesn’t want to take any chances, but Liara raising her voice in favor to use the gas had her reconsider. She agreed, but told her team to do what is necessary. 6 colonists were killed in the process.
After dealing with the Thorian on Feros, she shoots Shiala, seeing how she was tied to that creepy thing they've just taken out.
On Virmire, Hannah tried to talk Wrex down, but when he didn't follow her orders she felt she had no other choice but to shoot him. No one jeopardises the mission.
She didn’t fully trust the salarians and sent Kaidan with them, trusting he’s capable of taking care of himself if necessary. She took Ashley and Liara and they helped the salarian team by disabling various dangers, although she triggers the alarm at their end to ensure they she can proceed faster with her team. After leaving Ashley with the bomb, she was on the way to help Kaidan when his team was pinned down at the AA tower. When she had to choose between Kaidan and Ashley, she chose Kaidan because of her feelings for him, a choice that would haunt her for a long time, and she’s shocked and mad at herself for letting her feelings interfere with the mission.
The salarian captain, Kirrahe, seems like a decent guy to her after he expressed sympathy for Ash’s death and that they won’t forget what Shepard’s team has done there for them.
She sacrificed the Council without thinking twice because she saw Sovereign as the greater threat. When being asked who should be the new human Councilor she leaves without picking anyone, because to her, the Reaper threat is what she has to deal with.
Mass Effect 2
Waking up Hannah’s confused, even more so when she finds out she’s with Cerberus. She doesn’t trust Miranda, Jacob or the Illusive Man and she’s wondering if she is actually still herself.
She's glad to see Joker and Dr. Chakwas, but is initially distanced to the Cerberus crew.
When meeting Anderson she’s angry with him for not offering more help, angry at the Alliance for leaving her behind, but sees that Anderson still trusts her, trusts what she's doing.
When having quiet moments she’s in doubt about her relationship with Kaidan and reflects on it. She was never sure what exactly her feelings meant. Was that just a fling or something deeper?
Meeting Kaidan on Horizon was an absolute disaster for her and she feels like they would have needed more time in order to resolve things. But they didn't have that time, and she thinks it might be better the way it is. Feelings involved on important missions never work out well. When she receives Kaidan’s apology via e-mail she thinks about him again, about their time together, and cries in her cabin because she definitely feels she has already lost him and that their bond had been broken beyond repair anyway. By the end, she overcame her feelings for Kaidan and lets go of him.
She keeps things strictly professional with Miranda and Jacob, bonds with Jack, takes a liking to Mordin, is glad to see Tali and Garrus again as her views of both had changed drastically after ME1, likes Kasumi and accepts Zaeed until his loyalty mission, where he shows off his hotheadedness, but Hannah needs him. She’s initially suspicious of the assassin Thane, but eventually grows closer to him, too. She respects Samara, and they have some interesting conversations. She is aware she lets her guard further down by getting close to the crew, but doesn't regret it either.
After asking EDI’s opinion, the krogan they collected on the way is not let out of the tank because it’s too risky, same for activating the geth taken from the derelict Reaper.
Helping everyone with their personal affairs before heading through the Omega-4 relay is something Hannah deems as important, as she doesn’t want to risk anyone being distracted, like she was on Virmire.
She also helps Liara become the new Shadow Broker, rekindling their friendship along the way.
David Archer was sent to Grissom Academy, Hannah felt sick to the stomach what his brother did to him.
Everyone except Zaeed and Miranda are loyal in the end. Miranda was pissed because Hannah sided with Jack in their argument, and her decision to save the refinery workers left Zaeed still longing for revenge.
When finding the rest of the crew inside the Collector Base, they had already lost some people from the squad, and Miranda presses Shepard to not jeopardise the mission by sending them back to the Normandy with someone who could further help them with the Collectors. Shepard's torn here, as seeing these innocent lives right in front of her makes it hard to just go on. In the end she decides to send Zaeed with them, trusting the rest of her squad will still be enough.
Shepard destroys the Collector Base and gets out alive, while Jack, Miranda, Zaeed, Kasumi and Thane gave their lives to stop the Collectors.
Afterwards she helps Hackett's friend and destroys a batarian system in the progress to delay the Reapers for another few months. In the aftermath she meets James Vega, who is her only regular contact during her detention. She likes him, but as usual, she tends to keep to herself rather than talking a lot with him.
She aches to get out of there and fight for the galaxy, having more than a few restless nights.
Mass Effect 3
Hannah's at a point where she takes every help she can get to make the Crucible happen, to rally support against the Reapers. Even batarians and mercenaries. She knows what's at stake and that this is no time for old grudges.
The first hurdle after gaining the turian support was getting the krogan on board. She thinks about the offer from the salarian dalatress, but she hasn't decided anything when arriving on Tuchanka, because Eve showed her a different side of the krogan and she respects her.
But due to Mordin and Hannah previously destroying Maelon's research data, Eve died during the mission. Because of that and in order to also gain salarian support, Hannah pulls out her gun in the heat of the moment, trying to intimidate Mordin into letting it go. When he wouldn't budge, she either had the choice of stopping him or letting him cure the genophage with the dangerous Wreav in charge. Defeated, Hannah shot her old friend in the back, realising she goes to any lengths in order to win this war, doubting herself and her actions, grieving for Mordin back on the Normandy. Funnily enough it is Javik that has the right words for her in this moment and she draws strength from them:
She's on a path where morality doesn't matter anymore. She realises the Reapers will demand everything she has to give.
During the coup she had to face another tough situation. Being up against Kaidan, gun against gun. Things were already tense on Mars, where Hannah told Kaidan both he and Cerberus are in the past, although after her hospital visits she was sure they could put this whole thing to rest.
And during their stand-off, Kaidan came around and decided to trust Shepard. She was relieved he did. She wanted to believe she could've shot him if it was really necessary, but she was not sure. He still meant something to her and their past might have softened her too much.
Following Liara's lead to an asari monestary, Hannah stops Samara from shooting herself in order to save what little is left of their family, a topic very dear to her heart.
On Rannoch, she sides with the quarians because the geth VI repeatedly lied to her and she's afraid the geth might fall under Reaper control again, a possibility she doesn't want to take any chances with, and the quarian fleet wipes out the geth.
On Horizon, she couldn't help Oriana, and both her and her father died accidentally because Shepard hesitated to just shoot.
Towards the end Shepard is more tired and exhausted than ever, while still keeping appearances up in front of her squad, and she welcomes the shore leave while the Normandy gets ready for the last assault.
At this point she has doubts about herself and if she can do what everyone, including herself, expects her to do.
Additionally, the bond with the Alliance is still fragile, she follows her orders, but feels her loyalty to them is seriously damaged. The last three years have changed her a lot.
Her squad mates are what give her strength during these times and she knows she let all of them very close, some even too close, but she loves having them around. Her friendship with Liara, Garrus and Tali persists and grows deeper, and after breaking up with Kaidan to focus on the mission ahead they are also able to rekindle their friendship and trust.
After an initial dislike that EDI took over Dr. Eva's body, Shepard gets used to it and relies on EDI's crucial information, just as before. She doesn't want to judge her and Joker getting closer, so she tries to at least supports them.
Javik is the one who surprises her the most, actually mirroring many of her thoughts, and both of them have lost people close to them in the past. Neither Javik nor Hannah would want to reopen old wounds, and so Javik does not use the memory shard. She feels strangely connected to him, her distrust of aliens largely overcome at that point.
Despite liking James from her time in the brig, it created some tension between her and him when he wants to stay on Earth. After a Renegade-y sparring and both getting a bloody nose in the process, she feels like they've cleared the air, and likes that James has a nickname for her. She's intrigued by his flirting and wants to show him she can play this game, too. She supports him going for N7 and notices they have quite some things in common, growing really close in the process. She eventually traps herself in their flirting game and is hurt when he rejects her while visiting her in the apartment on the Citadel. And despite knowing that James respects regs and his own fraternization rules way too much, Hannah pursues a one-night stand with him at the party to still her loneliness and to feel something good, but also finally admits to herself that the other reason she did it is because she had started to fall for him and could not let go.
However, she knows she can't allow herself to let those feelings flourish any further and focuses on the mission instead.
Together with James and Javik she fights through London and makes a run for the Citadel beam, until James is badly hurt in the process. All she cares for is getting him out alive, calling in the Normandy for evac, jeopardising the mission once again.
It hurts her they have to part ways, and seeing him reach out to her, but she has to finish this on her own. Managing to get up to the Citadel, Hannah chose to destroy the Reapers and took a breath in the end.
The headcanon part 
Well, it's a super sappy ending... I initially wanted to let Hannah die, and the thing with James was something physical only after the Kaidan disaster, but a song and its lyrics I heard changed my mind, and from there I just got stuck with this idea to let them fall for each other and have a future together. It just happened somehow, and I couldn't let go of that idea. I was intrigued by how James held back because of his respect for Shepard, the regs and his own fraternization rules during the Citadel DLC and I headcanon that during their night, Hannah shows her true self to James and also tells him about her past, which allowed for building up a very slow admittance of feelings after a drunken, messed up night on their end. And so I tried to work out how they could still end up together.
I thought they both deserve some happy times after this war
Oh, and she ended up being pretty much 50/50 on the Renegade/Paragon part.
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