Agents of S.H.I.E.L.D., ABC
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Caution: So many spoilers!
So, yeah... last season, it turned out that Garrett was the Clairvoyant. He didn't actually have psychic powers, or anything, but used access to SHIELD databases or whatever, to learn various secrets and stuff. Anyway, like I said before, Coulson's team defeated him. However, another thing we learned last season was that Garrett's former protege, Grant Ward, is also a Hydra sleeper agent. (He's not really loyal to them, but rather to Garrett. But Garrett's gone now, so it's unclear where Ward's loyalties will lie, going forward, except that he claims to want to help Skye.) The one thing that is clear is that no one on Coulson's team will ever trust him again, because he caused a lot of trouble for the organization, including killing Victoria Hand and later, Eric Koenig. But he was finally captured, and he starts out this season as a prisoner of Coulson's team (though he eventually escapes). Also last season, Nick Fury made Coulson the new Director of SHIELD... which now mainly seems to consist just of Coulson's team, though there may be other agents scattered around the world. Agent Triplett (who was as shocked as anyone to learn that his S.O., Garrett, was a Hydra agent) is now a member of Coulson's team. Also joining the team this season are agents Lance Hunter and Alphonso "Mack" MacKenzie. (And Isabelle Hartley, played by Lucy Lawless, though she dies in the season premiere, and will be seen in a flashback later in the season.) Of course, SHIELD is still considered a terrorist organization, so they're sometimes in conflict with Glenn Talbot, who's now a brigadier general.
Well, there are lots of things going on. Simmons starts the season working undercover within Hydra, as a spy for Coulson. She eventually returns to SHIELD, along with yet another badass agent, Bobbi Morse (who had also been undercover in Hydra, and who is Hunter's ex-wife). But first... Fitz suffered brain damage last season, because of something Ward did, so this season he struggles to remain useful. During Simmons's absence, he frequently has conversations with a hallucinatory image of her. Meanwhile, there's a mysterious and dangerous obelisk which Hydra (under the direction of Daniel Whitehall) wants for some unknown purpose. The Obelisk changes hands a few times before Whitehall finally obtains it. (Raina has it, for awhile, so she's sought by both Hydra and SHIELD.) Also, we meet a doctor named Calvin "Cal" Zabo (Kyle MacLachlan), who turns out to be Skye's father. He desperately wants to reunite with his daughter, but she wants nothing to do with him, because of the many monstrous things he's done. But they have a common enemy in Whitehall, who is responsible for the death of his wife (Skye's mother, played by Dichen Lachman). Eventually, Coulson kills Whitehall, which infuriates Cal, who wanted to kill Whitehall himself. Also... throughout the first half of the season, Coulson suffers a compulsion to draw (or carve) symbols or diagrams that he doesn't understand, which was caused by... well, I guess by the means by which he was brought back to life. It's weird and complicated. But it involves aliens called Kree, who had visited Earth a long time ago. Eventually, Coulson learns that what he's been drawing is a diagram of an ancient Kree city, and the Obelisk is a key to that city. So there's a race between SHIELD and Hydra to find the city. (It's buried beneath what is now San Juan, Puerto Rico.) And we eventually learn the true identity of Whitehall, which I won't spoil, but he had experimented on the Obelisk a long time ago. And um, Cal apparently knows a lot about the Obelisk, which is actually called the Diviner. And the purpose of the Diviner is to determine who is worthy of entering the city (i.e., descendants of ancient humans who had been genetically engineered by the Kree). The worthy ones turn out to be Skye and Raina, who are transformed by a strange mist, which will be explained more in the second half of the season. But anyone who is exposed to the mist but isn't "worthy" is killed, rather than transformed. And this is what happens to Triplett.
During the show's midseason hiatus, its timeslot was filled by season one of Agent Carter.
In the second half of the season, everyone is mourning Triplett's death, and also SHIELD strikes back against Hydra, killing several of their top people. Meanwhile, Raina's transformation involves growing a lot of spikes, making her think she looks like a monster. But she's taken away by a man named Gordon, who has no eyes, and who can teleport. Also, Ward is now working with a former SHIELD agent named Kara Palamas (aka "Agent 33," played by Maya Stojan, whom I know from Castle). She had formerly been brainwashed by Whitehall into becoming a Hydra agent, and now Ward is helping her seek vengeance against SHIELD (for some reason). Also, Skye's transformation has no visible changes, but she now has the ability to cause earthquakes, which she can't control. So she tries to hide this fact at first, but eventually her friends find out and try to help her. We also learn that Mack and Bobbi are keeping a secret from Coulson and the others, and might actually be working for enemies of SHIELD. And we meet May's ex-husband, a psychologist named Dr. Andrew Garner (Blair Underwood), who used to work for SHIELD and is still willing to help out, from time to time. This includes psychoanalyzing Skye, after which Coulson sends her to a secret safe house. And... we see some flashbacks to different things, including the mission where May got the name "Cavalry." Meanwhile, we finally learn that Mack and Bobbi aren't exactly traitors; rather, they're working for "the real SHIELD," that is, a board of high ranking agents, led by Robert Gonzales (Edward James Olmos, best known to me from Battlestar Galactica). The people on this board don't trust Coulson (and they feel it was wrong of Nick Fury to keep so many secrets even from the people who worked for him). Another important member of the board is Anne Weaver (who had been seen in season one, as head of SHIELD's Academy of Science and Technology, prior to Hydra's attack.) Their headquarters is an aircraft carrier called the Iliad. Conflict eventually breaks out between the two factions of SHIELD, including attacks by Gonzales's people on both the Playground and the safe house where Skye is. However, Gordon shows up at the safe house and teleports Skye to safety.
He takes her to an idyllic hidden location called Afterlife, where there are lots of people with powers, who are called Inhumans (which is what Skye and Raina and Gordon are). Each of them has a unique power, which were activated in a similar way to Skye and Raina. (The transformation is called "terrigenesis," which is triggered by mist produced from Terrigen crystals.) Skye is befriended by a guy named Lincoln Campbell, who has electrical powers. (He's played by Luke Mitchell, whom I know from The Tomorrow People.) And he helps her learn to control her own power, which is more complex than she originally thought it was. Skye also finds out that Raina is there, and her power is precognition. And Skye meets the leader of the Inhumans, a woman named Jiaying, who has healing powers. (Viewers who have seen earlier flashbacks will realize that she is Skye's mother, but it's awhile before Skye learns that.) Skye also learns that Cal is at Afterlife, which disturbs her. But she slowly begins to realize he's not a complete monster. (It surprised me, incidentally, that Jiaying was alive, but it turns out that after Whitehall had apparently killed her in the most horrific fashion, Cal had... fixed her, something that was only possible because of her power. Still, even if she wasn't really dead, Cal had more than ample reason to want to kill Whitehall.)
I should probably mention that sometime near the end of the season, Hydra destroys the Bus. And throughout the season, we occasionally see a Hydra agent named Bakshi, who had been Whitehall's second in command. He was a candidate to become the new leader of Hydra, but he eventually dies. But not before we see him talking with another high ranking Hydra agent named List. One of the things they discuss is yet another Hydra agent, Baron von Strucker, whom we don't actually see. But various people on the show make mention of things that will tie into the movie Avengers: Age of Ultron, which came out two weeks before the end of season two. (Naturally, I didn't get to see it, but nothing that happens in the final two episodes really spoils it, even though characters will make some vague allusions to the events of the movie, in those eps.) Anyway, Coulson eventually makes peace with Gonzales, so the two factions can work together against their real enemies. (Coulson will be director, with Gonzales's board being his oversight council, like the World Security Council had previously been for Nick Fury.) SHIELD learns the location of Afterlife, and Gonzales goes there to negotiate with Jiaying, who hands Cal over to SHIELD. But she has a bunch of Terrigen crystals, and uses one on Gonzales, which kills him. She then shoots herself with his gun. In the season finale, some of Jiaying's people hijack one of SHIELD's Quinjets to stage an attack on Afterlife, in order to start a war. All the Inhumans believe SHIELD attacked first, including Skye. But she later realizes the truth because of a vision Raina had told her about. She didn't believe Raina at first, but realized it was true when she saw her mother kill Raina. Meanwhile, Ward and Kara kidnap and torture Bobbi, for reasons. And the Inhumans attack the Iliad, which has something on board that they want. Cal takes a serum he'd created, which has a sort of Mr. Hyde effect. He intends to kill as many SHIELD agents as possible, but Coulson convinces Cal to join him against Jiaying, for the sake of Skye. And um... there's just so much going on in the episode, on at least three different fronts, so I couldn't keep track of everything. But Gordon, Jiaying, and Kara are all killed. And Coulson suffers a loss of his own, the nature of which I don't want to reveal. And Cal has his memories altered. Coulson puts Mack in charge of SHIELD's alien tech, and puts Skye in charge of people with powers. May takes a break from SHIELD. Ward begins gathering whatever remaining Hydra agents he can find, to become their new leader. And... I'll hold off on spoiling what happens in the final scene, until I have to reveal it next season...