A Croft's work is never done
WARNING: Spoilers for the comic, obviously, with additional spoilers for the first game throughout.
Returns to Yamatai to save Sam from a murderous cult
Apparently what happens on Yamatai doesn't stay on Yamatai. Before the engines have even cooled following Lara's return to London after the events of the reboot, she discovers she and her friends are being stalked by a mysterious cult in pursuit of cursed artifacts (like a solid-gold dragon statuette) that they pocketed during their harrowing island vacation.
Of course, Lara's pretty sure she was too busy stabbing people and fleeing for her life to steal anything, but no time to worry about that - not only is she being pursued by mythical calamities, but the cult kidnaps Lara's dear friend Sam and takes her to Yamatai as part of their plans. The remaining members of the Endurance crew return to save her, with disaster on their tail.
Barely dodges becoming a blood sacrifice for a resurrection ritual
Of course, that's exactly what the cult wanted. They're in fact Solarii-worshippers and are trying to bring their messiah, Mathias (you remember him), back from the dead so they too can be blessed with his magic. To do that, they need to perform a convoluted ritual involving blood sacrifice (which is what set off the calamities, signals from the planet that shit's going down). Since Lara is the one that killed Mathias in the first place, she is meant to be their unwilling donor, and Sam's kidnapping was all just a plot to lure her into their grasp. How do a bunch of well-dressed businessmen know about the magic-wielding leader of a bunch of shipwrecked soldiers on an uncharted island? Don't worry about it.
But, naturally, things don't go according to their plans - Lara and company escape, most of the cult members are crushed to death as a temple collapses around them, and the last of the calamities takes out a man holding a gun to Lara's head. Happy ending!
Travels to Pripyat, Ukraine to rescue Alex's sister from an assassination attempt
During her second trip to Yamatai, Lara sees a hallucination of Alex - one of her friends who didn't survive the game - speaking to her about protecting someone back home. She chalks it up to inhaling the island's natural gas. But when the same hallucination pops up during a hike in the Welsh countryside, telling her to protect someone dear to him who's in trouble, she takes it a bit more seriously.
Getting a clue off of a watch that belonged to Alex's father (which she got from the hallucination?) Lara goes searching for Alex's sister Kaz. She recently went missing near Pripyat, Ukraine, a real ghost town in the Chernobyl Exclusion Zone. Though, missing isn't quite the right word. When Lara eventually finds Kaz - still safe and sound and armed to the teeth - she discovers that Kaz knows about the killers, because she used to be one of them.
and discovers the nefarious organization Trinity
Specifically, Kaz used to belong to a powerful shadow organization known as Trinity (name-dropped in both the reboot and promotional material for Rise of the Tomb Raider), but left when things got too heavy. She started a new life in America, marrying a woman named Lucya. But apparently Trinity's the kind of group you only leave in a pine box - they killed Lucya and, having no place to go, Kaz escaped to Pripyat, where Lucya's family still lives and gets paid to maintain the ruins of Chernobyl.
Unfortunately, a little radiation doesn't stop Trinity. They send one of their most aggressively sadistic agents to finish the job, and when he and Lara nearly kill each other, she officially earns a spot on Trinity's shit list. Sparing no expense, they send a military helicopter to take out Lucya's family home and put a rocket in it, since they prefer to be thorough. However, they're not prepared to face a Croft: Lara empties a machine gun into the pilot, crashing the helicopter and burning Agent de Sade to death, before offering Kaz a new life in London and a spot in her flat.
Is stalked by a dying member of Trinity who wants to make her his protg
But what kind of evil-corp would Trinity be, if that was the end of it? Though their man in Ukraine miraculously survived with severe burns to his whole body, he's in no shape to pursue Lara himself. For that, Trinity sends a less obviously fiendish agent (who is facing down his own mortality due to aggressive cancer) to finish Lara and Kaz off.
However, after hearing what she's capable of and seeing her beat down a pair of muggers in the street, he becomes infatuated with Lara and resolves to take her on as a protg as a way to close out his life. The man from Ukraine takes such exception that he leaves the hospital while barely healed, resolving to deal with both of them himself.
Almost dies on stage, and for real
Not that Lara's aware of any of that. While all that's going on, she's caught up in rehearsals for a production of Pride and Prejudice directed by her friend Jonah, who talked her into a starring role (no, really).
It's only on opening night that she gets a rude awakening: Trinity's Ukraine agent tells her, via a ransom note, to meet him in the London underground or Kaz dies. Lara complies, and while she fares well in a fight given her full Georgian dress, she's only able to finish the job with the help of her admirer/stalker. He offers to make her a full member of Trinity, and when Lara refuses, he has no qualms letting himself get hit by a train. Lara goes back and finishes the play after that - though, obviously, in a different dress.
Finds out a friend she thought was dead has been kidnapped, reveals the Croft estate isn't in her control, films a fake movie
Because there's no end to the reminders of what happened on Yamatai for Lara, after her brush with Trinity, she gets a knock on her door from somebody who knew the surly helmsman Grim. Or, rather, they know him and provide a tape of him at their compound in the Mexican jungle, which Lara finds mighty confusing as she saw him die. That doesn't seem to faze her callers however, who demand a ransom for Grim's life.
The big-hearted person Lara is, her first thought is to pay the ransom in full. However, it turns out her uncle is the executor of the Croft estate, and given Lara's dangerous globetrotting escapades, he doesn't feel she's of a sound mind to handle her inheritance. With that option off the table, Sam comes up with a brilliant idea: travel to Mexico under the guise of filming a documentary on the Chupacabra. With few better options, Lara, Kaz, Sam, and Jonah venture forth to rescue their not-dead friend.
Finds out Grim isn't Grim
As things are wont to do when Lara Croft is involved, their simple plan quickly gets complicated - Sam starts having unexplainable blackouts, which leads to a fight when Lara refuses to let her keep going in her condition. Under cover of night, Lara sneaks away to deal with the kidnappers herself.
Once again, her luck doesn't pan out, and she ends up being captured and thrown in a prison-hole alongside Grim. Or rather, not-Grim. When they come face-to-face, Lara discovers the person in the video is actually Grim's brother, who was captured by Mexican eco-terrorists while sailing his brother's boat in international waters, and mistaken for a man the Croft family would pay dearly to protect.
and that his kidnappers know the Crofts all too well
It seems odd that a random terrorist group would know about the Croft coffers, but it isn't random at all - their leader is an old lover of Lara's father who he met during an expedition to study Mayan ruins. While she acted as his guide, he told her all about his adventures, revealed the extent of the family fortune, and got to know her in a Biblical fashion before disappearing, never to be seen again. Now with a lot more years under her belt, she's cynical enough to take advantage of the opportunity when she gets ahold of a Croft family friend, knowing how much wealth comes along with the name.
With no interest in dealing with her father's old baggage, Lara sets up a diversion and escapes with Grim's brother in tow. That leaves the terrorists stumped as they watch one of their ships sail, Viking-funeral-style.
Discovers that something is very wrong with Sam
While everyone makes it out of Mexico safe and sound, Lara and Sam's friendship doesn't, and Sam remains dismissive and hostile toward Lara weeks later. Given that Lara finally gets some downtime to let the traumas of the last year properly eat away at her, not having her confidante does a number on her emotionally, and she seriously considers disappearing without a word or another globe-trotting expedition to keep the memories at bay.
Of course, those unexplained blackouts were bound to come up sooner or later. Lara eventually gets a phone that Sam has been arrested for an assault that she doesn't remember committing, and is being held at the local jail. When Lara goes to visit her, however, she discovers that Sam isn't entirely home - she talks and acts as though she's possessed by something, and though Lara briefly gets through to her, Sam storms off before Lara can get a grasp on happening to her. That just about wrecks Lara mentally, and she immediately heads home to pack and run away from her problems.
Does NOT go globetrotting in search of mythical artifacts
You'd think that's where the comic leaves off and Rise picks up, which it does, but not before throwing in one last wrinkle. At the last moment, Lara decides not to leave, because she realizes it won't actually fix what's eating away at her. Instead, she decides to write about everything that happened in Yamatai (with an eye for public exposure, even), to both help herself and ensure that her friends won't be forgotten. And that's it. From there, it's on to Rise of the Tomb Raider.
How well Lara's writing efforts turn out are anyone's guess until then - though, given that she feels no one would believe what she's been through when Rise opens, not very well is probably the answer. Plus, something has to prompt Lara to take up that world-circling, myth-hunting adventure she originally decided against. Is writing how Lara finds herself? Does she decide that adventures and musings aren't mutually exclusive? Is this really how Sam makes her grand exit? Seems Rise has more to answer than anyone realized.
