It’s been three months since an alien artifact released a mist that literally changed the lives of the Agents of SHIELD. One of their own has died, while another is undergoing a major change that may make her a threat, rather than a friend. There’s still HYDRA, and whatever Raina has become. Things are different now.

***** SPOILERS BELOW *****

This is a disaster.
No, it’s an origin story.

Pilot from Agents of SHIELD

That’s what Mike Peterson said when the Extremis inside of him started to take over his body, giving him super-strength…but also almost killing him. It changed him, turning him into a weapon that he never wanted to become.

More than a year later, the Terrigen Mist has invaded Skye’s body, and changed her into something she doesn’t understand, it also killed Tripplett.and that has scarred the team deeply. This is the start of a dramatic arc where SHIELD will not only be in a battle between good and evil, but between forces that will not understand each other. At the center is Skye, who will be urged to embrace her new form and renounce SHIELD.  At least, that’s what her dad Cal Zabo (Kyle MacLachlan) expects.

The second half begins in 1983, with a teenage boy named Gordon trying to teleport his way out of a room. It’s difficult, since he has no eyes.  He’s the younger version of the man we saw at the end of the previous episode back in December. He just got misted, and is having problems with the after effects. A Chinese woman named Jaiying (Dichen Lachman), Skye’s mom, tries to comfort the boy. She is hopeful she can help him accept his new powers, and embrace his new life.

More than 20 years later, Skye is quarantined after the events of the temple, including her being misted. She still has nightmares of seeing Triplett being charred to death. Coulson has had those nightmares, too. He thinks the Diviner caused the quake, and nearly killed everyone, Mac has recovered from the affects of the Diviner, but he’s still very angry over what has happened. So is Skye, because she blames herself. Coulson says it’s still a war, and while HYDRA is looking for a new head, he’ll crush them. He’s become very obsessed with this, almost as much as the obsession of drawing those alien markings.

Speaking of which, the HYDRA Board is discussing who should be the new boss now that Whitehall is gone. There’s a Baroness (Kathryn Leigh Scott), a Sheik, a banker, a guy named Octavian Bloom (Fred Dryer)  and Dr. List (Henry Goodman). They honor Whitehall, and discuss what will happen to Bakshi (Simon Kassianides) since he’s a prisoner of SHIELD. They also mention Von Strucker, who is still a major player in HYDRA. They all agree whoever gets rid of SHIELD will be the new boss.

What happened to Raina (Ruth Negga)? The mist was not kind to her. She has turned into a female porcupine, and killed two SHIELD scientists. Simmons is very concerned because she thinks maybe Raina has been infected, and could possibly infect others. She even admits putting her down may be necessary. However, it becomes apparent that Simmons thinks people with powers are the real threat, whether it’s Mike Peterson, Donnie Gill or Creel . She even fears the Avengers because they attracted the Chitauri. This proves that even scientists can fall victim to irrational fears, just as Zabo thinks people will fear Skye, sooner or later.

Mac is still very angry over Tripplett’s death, and blames Coulson for his obsession for dealing with HYDRA and looking for that alien city. In fact, his anger causes Skye’s heart rate to go through the roof and starts a tremor. Coincidence?
Coulson arranges to give Bakshi to General Talbot (Adrian Pasdar), but it seems they’re ambushed by HYDRA’s men, while he is picked up by Lance.  Actually, it’s part of a clever scheme where they hope to turn Bakshi against HYDRA for cash…and his life.

Zabo, Skye’s dad, is hiding in a tanker. He’s not alone. Raina is there, and we get a good look at what the mist has done to her. She’s mad, because Skye got the incredible transformation and not her. Zabo is happy that Skye has undergone the transformation, but fears once Skye’s powers are released, SHIELD will put her in a cage. He thinks maybe he should get his friends together to convince Skye to go back to her dad, and ruin SHIELD, too.  As for Raina, she’s stuck in her new form, and he doesn’t care.

Leo Fitz, though, does care. He confronts Skye when he discovers her heart rate was 300 beats per minute at the time of the temple collapse, which he says is “inhuman.” He can’t understand how she survived in the center of destruction, and that he can’t pass it off as something his damaged brain can’t understand. He also notices another tremor, and the lamp above Skye breaking. It confirms that there’s nothing wrong with his head. She has been transformed. However, he’s willing to keep it a secret until things calm down. It’s likely, though, the secret will not cooperate.

While Lance and Morse are waiting for their part in SHIELD’s plan discuss why she’s getting closer with Mac. She claims they’re part of a support group that’s helping them deal with the stresses of the job. The plan with Bakshi does work. Most of the HYDRA board do knock each other off, even using that poison from the Diviner. Bloom is also killed, which means HYDRA is crippled, for now.

Meanwhile, as Raina contemplates suicide, a SHIELD crew surrounds her. She tells them to kill her, or she’ll make them do it. She is suddenly saved by a man with no eyes who can teleport. Gordon (Jamie Harris) is all grown up, and he tells Raina he’ll show her the way, as they both vanish.

Finally, we find out why Mac wanted to make that RC version of Lola. He and Morse want to find Nick Fury’s Toolbox and blueprints from the base, and they seem to be working for someone. If it’s not HYDRA, than who is it?

It seemed this episode may have been stuffed with a lot of plotlines: Skye’s secret, Raina meeting a fellow Inhuman, HYDRA trying to recover, Coulson hoping to defeat them, and whatever Morse and Mac are planning. Two of the plots could have been delayed for a week or two, but it looks like the show wanted to start fast with several plots to regain our attention after Agent Carter. Besides, we already know Edward James Olmos will soon make an appearance. Could he be behind the search for the Toolbox?

Also, one person is missing:  Grant Ward and his new friend, Agent 33. How will they be part of the second half? Will they help HYDRA, Zabo, or someone else? It’s safe to say they’ll be heard from again.

Next week, Lady Sif is back, but she has memory problems. She does play a part in the fate of Skye, now that her powers are no longer a secret.

Entertainment Weekly has articles about what Morse and Mac are doing, and Skye’s new powers.

Marvel’s Agent’s of SHIELD airs on Tuesdays at 9/8c on ABC. Wathc full episodes on ABC.Go.com, HULU Plus and On Demand (check with your local cable provider).