Agents of S.H.I.E.L.D., on ABC
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Caution: So many spoilers!
So, the thing that was on the Iliad was something called the Monolith. The final scene of last season was the Monolith morphing into a portal (or something), which reached out and grabbed Simmons and dragged her away. So this season, Fitz is obsessed with finding a way to reactivate the portal and get her back. I also need to mention that last season, Skye learned that her real name is Daisy Johnson. At first she didn't want to use that name, but this season she has embraced it, so her friends have to get used to it (which takes them awhile). And Jiaying had released terrigen into the world's water supply, or something, so now there's an epidemic of people turning into Inhumans, and often being unable to control their powers. So SHIELD is tracking them down to stop them from hurting anyone, but also to protect them, train them, and possibly recruit them into SHIELD (but first they must pass psych evaluations from Andrew). And I guess any Inhumans who work for SHIELD will be called "Secret Warriors." However, there's an agency of the U.S. government that is also tracking down Inhumans, and often manage to capture them before SHIELD can arrive. They're called the ATCU (Advanced Threat Containment Unit), and they're led by Rosalind Price (Constance Zimmer). SHIELD does manage to get one man, Joey Gutierrez, before the ATCU gets to him. (His ability is kind of like metalbending, I guess.) Daisy is also looking for Lincoln, who is on the run. There's also a mysterious, monstrous Inhuman called Lash who is killing other Inhumans, for unknown reasons. Meanwhile, Ward recruits a young man named Werner von Strucker (son of Baron Wolfgang von Strucker) into Hydra. (But he ultimately turns out to be a lot less important than I expected.) And May eventually returns to SHIELD. Oh, also I should mention that Coulson's team now has a new plane called Zephyr One (or just "the Zephyr"), which is a replacement for the Bus.
Checking Wikipedia to help me compose this season's recap, I find that Fitz got Simmons back at the end of the second episode, which is sooner than I remembered it happening. Still, there'll be more to learn about that later. Meanwhile, Hunter and May track down Ward, and Hunter tries, but fails, to kill him. This apparently leads to Ward having his people kill Andrew, for which May blames Hunter. In the fifth episode, we see what happened to Simmons during the six months she was missing. She was on a desolate alien world, where she met an astronaut named Will Daniels, who had been sent there through a portal by Hydra in 2001. (He and a team of scientists believed they were on a mission for NASA. Now all the other members of his team are dead, so Will's been alone for years.) There's also some malevolent being on the planet that Will just calls "It." Anyway, Will captures Simmons, unsure at first if she's real, but eventually they become friends, and later, lovers. At the end of the episode, we see that Simmons has been relating all this to Fitz, because she needs his help going back to that world, in order to rescue Will. Naturally, Fitz has conflicted feelings, because he's in love with Simmons. But he doesn't hesitate to agree to help, because... you know, he's awesome.
Eventually, SHIELD and the ATCU begin working together, though each side remains suspicious of the other. But Coulson and Price begin to become friends, and then lovers. (Which still doesn't end the distrust.) Also, we eventually learn the true identity of Lash, but I don't want to spoil that. But I will say that he's finally captured by SHIELD, and delivered to the ATCU (where Inhumans are kept in suspended animation, while their scientists search for a way to "cure" them). Also, there's a man named Gideon Malick (Powers Boothe), who I guess was first seen in The Avengers, as a member of the World Security Council. He's now an adviser to U.S. President Matthew Ellis, and spearheaded the creation of the ATCU, as a replacement for SHIELD. But we learn that he's actually one of the heads of Hydra, and he eventually forms an alliance with Ward. And we learn that rather than trying to cure Inhumans, Hydra's moles inside the ATCU were trying to create more of them. This is something Price was unaware of, and after convincing Coulson of that, they make plans to take down Malick. But before they can, Ward kills Price (mainly to make Coulson suffer). And we learn that the entity on the alien world is an ancient Inhuman, and the whole purpose of Hydra's existence, over the centuries, has been to find a way to bring it back to Earth, as a general for an Inhuman army that Hydra is currently assembling.
Hydra kidnaps Fitz and Simmons, and tortures Simmons until Fitz agrees to help a team sent through another portal, since only he knows how to return to Earth from the alien world (which is called Maveth). However, he promises Simmons the only thing he'll bring back is Will. The team is led by Ward, and Coulson manages to follow them through the portal, planning to kill him as revenge for Rosalind. Meanwhile, he leaves Mack in charge of SHIELD, and Mack sends two teams into Hydra's stronghold where the portal is. They intend to rescue Fitz and Simmons, as well as the Inhumans that Hydra had used the ATCU to capture, and to make sure Hydra doesn't bring the ancient Inhuman back to Earth. (Lincoln and Gutierrez are now both working with SHIELD. Also, I guess Daisy and Lincoln are a couple, now.) Simmons manages to escape on her own, and discovers the Inhuman containment pods, including Lash, whom she frees so that he can protect her from Hydra. (I guess this would be a good time to reveal that Lash is Andrew, who hadn't actually been killed by Ward's people. However, May had helped capture him- actually, she shot him, not knowing that it wouldn't kill him- to stop him from killing Inhumans. Because he was losing his ability to think rationally.) Anyway, he kills some Hydra agents, but he also later kills all the captive Inhumans, and escapes. Meanwhile, Fitz finds Will, and the two of them plan to return through the portal without Ward or any of his people. But Fitz discovers it's not Will, it's actually "It," and had killed Will and taken over his body when Simmons originally escaped from Maveth. (It also now has Will's memories). So they fight, and Fitz seems to kill him (which makes the entity seem a lot less formidable than Hydra thought it was, but... we'll soon see that it's not). Coulson finds and kills Ward, then he and Fitz return through the portal. SHIELD destroys the stronghold, but not before Malick gets away. However, the midseason finale concludes with Malick being confronted by Ward, apparently. (So I guess that means "It" took over Ward's body and escaped through the portal without anyone realizing it.)
During the show's midseason hiatus, its timeslot was filled by season two of Agent Carter.
In the back half of the season, SHIELD recruits an Inhuman from Colombia, named Elena Rodriguez. She has super speed, but with very limited range; after a single heartbeat, she bounces back to where she started. This leads to Mack calling her "Yo-Yo." She stays in Colombia, but SHIELD can call her in whenever they need her for a mission. Meanwhile, President Ellis makes General Talbot the new head of the ATCU. However, Ellis unofficially reinstates SHIELD as a legitimate agency. The public still perceives them as terrorists, so for now it has to remain secret. But while the ATCU is the public face of the government's attempts to deal with Inhumans, the group is now under the jurisdiction of SHIELD, which means Talbot reports to Coulson. Meanwhile, Malick convinces a group of world leaders to build a sanctuary for Inhumans in Siberia. Bobbi and Hunter secretly follow Malick there, but they end up being captured. In the end, they are forced to resign from SHIELD, in order to protect the secret that SHIELD still exists.
Another problem that arises is an anti-Inhuman hate group called the Watchdogs, who steal something from an ATCU facility. They then destroy the facility, so that no one would know what was stolen. However, it turns out that the Watchdogs are backed by Hydra. In another episode, there's an Inhuman named Charles Hinton, who has visions of people's future deaths when he touches them, visions that are shared by the person he's touching. This happens to Daisy, who sees... a scene set in outer space, aboard a Quinjet. But it's unclear whose death she's actually foreseen, hers or some other SHIELD agent's. Later, Daisy and Lincoln track down a potential Inhuman named James, who had formerly been at Afterlife, but hadn't been transformed. He refuses to join them, but he does give them a mysterious Kree device of some sort. Meanwhile, the ancient Inhuman who is now inhabiting Ward's body is called Hive. And while Malick was glad to have him on Hydra's side after so many generations of trying to retrieve him from Maveth, a rift eventually grows between Hive and Malick. And Malick's head of security, an Inhuman named Giyera (who has telekinetic powers), switches allegiances, now serving Hive. At one point, Giyera takes control of the Zephyr, so the Secret Warriors have to save the SHIELD agents. They also capture Malick, who reveals some things SHIELD didn't know about Hive, including that he can "sway" Inhumans by infecting their minds, so they'll be loyal to him. When someone kills Malick at SHIELD's base, they realize Hive had infected a member of the team, so there's lot of paranoia about who it might be. Lincoln is the prime suspect, but it eventually turns out to be Daisy, who steals the Kree artifact they'd gotten from James and takes it to Hive. Later, Hive gives James terrigen to transform him into an Inhuman, then sways him. (His new power is, like, creating fire within objects, or something.) Oh, and there's an Inhuman named Alisha Whitley (who can replicate herself). We first saw her in season two, in Afterlife. She later became an ally of SHIELD, though not an actual agent. Anyway, Hive now sways her, too.
Fitz and Simmons seek a scientist named Holden Radcliffe (John Hannah), whom they hope could find a way to counter Hive's power and free Daisy from his sway. But Hive's agents kidnap Dr. Radcliffe, and take him to a town Hive had bought with the fortune he inherited upon Malick's death. Hive wants Radcliffe to recreate the Kree experiment that had created the first Inhumans, thousands of years ago. Meanwhile, before Malick was killed, he had provided intel that Talbot and the ATCU now use to wipe out all of Hydra's remaining bases. Also, Fitz and Simmons finally start a romantic relationship. Anyway... Radcliffe's first attempt at the experiment fails, because he needs Kree blood. So Hive uses James's artifact to summon two Kree warriors, who try to kill him (and they do kill Alisha). Daisy kills one Kree and starts draining his blood, while Hive destroys the other (which means the body provides no blood for the experiment). SHIELD sends a team to Hive's town, and Mack manages to eliminate the blood of Daisy's Kree. But later, after SHIELD retreats, she offers up her own blood, since it had been infused with Kree blood in season one. So, Radcliffe's second attempt to create Inhumans sort of succeeds. He turns Watchdogs into nearly mindless, but very strong, mutants, whom Hive is able to sway. (I guess they're called "Primitives.")
Around this point in season 3, the movie Captain America: Civil War takes place. I wouldn't get to see it until after season four, but the show mentions an aspect of the movie called the Sokovia Accords, which I guess requires people with powers, such as Inhumans and the Avengers themselves, to be registered and... whatever. I dunno all the details. But there is now some question as to whether the Secret Warriors should be registered. Talbot's for it, Coulson is against it, and I guess he manages to convince Talbot of the need for secrecy. Also, Talbot informs him that what had been stolen from the ATCU facility was a warhead. And now Hive plans to use it to disseminate a pathogen Radcliffe had created in the atmosphere, which could turn all humans (not just descendants of the original Inhumans) into Primitive Inhumans that would be immediately swayed. Meanwhile, Lincoln contacts Daisy and she hacks SHIELD's security system to help him steal a Quinjet so they could be together again. But when the Quinjet arrives, Lincoln's not aboard it: Lash is. Somehow, he frees Daisy from Hive's sway, and she takes the Quinjet back to SHIELD. However, James kills Lash.
In the two-part season finale, SHIELD sabotages Hive's attempt to launch the warhead. They also capture Hive, much to the relief of Radcliffe, who joins their side. However, James and Giyera get away with the warhead. After getting Hive back to the Playground, a bomb is smuggled into the base that releases the pathogen, turning a number of random SHIELD workers into Primitives, who release Hive from stasis. He steals the Zephyr, and James and Giyera bring him the warhead, planning to fly it high enough to release enough of the pathogen to turn, I guess like a few continents of people into Primitives. And... May and Fitz are also on the Zephyr, and Fitz kills Giyera. The rest of Coulson's team takes a Quinjet to intercept the Zephyr and try to stop Hive. They get the warhead onto the Quinjet, which will take the warhead into space where it would detonate without spreading the pathogen. Daisy wants to go on the Quinjet, but Lincoln goes instead, to ensure Hive can't interfere with the plan. In the end, Lincoln and Hive both die, fulfilling Daisy's earlier vision. (But for awhile there, there seemed to be several possibilities of who would be on the Quinjet. All we knew from the vision was that there was a crucifix onboard, which Yo-Yo had given to Mack earlier, and leading up to the climax, several different people had the crucifix before it finally ended up with Lincoln. Damn writers, with your mindscrews... you think this is a game?!) Then there are some brief scenes set six months later, which I won't spoil, until next season. (It's not like I have a clear idea of what the scenes meant, anyway.) But, man, I feel like I've spoiled WAY too much about this season, already. (Trust me, though, I've left out a lot.)