So far this season, trust within SHIELD has been slowly falling apart, mostly due to lies and fear. Skye’s earth-shaking power is accelerating the damage.

Now, a dark secret is making things worse, and it causes Skye’s dad to do something drastic. We also find out who Mack and Morse really work for, and it’s not HYDRA.

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

SHIELD’s main goal is to protect the world from any serious threat, but how they do it isn’t always noble. This week’s episode revealed that it had a “Gifted Index” to track those people who maybe a serious threat. Cal (Kyle MacLachlan), Skye’s dad, tracks some of them down as part of a plan to get her back, and expose skeletons in SHIELD’s closet.

However, they aren’t Inhumans, but people who got their abilities though other means. Karla Faye Gideon (Drea De Matteo) grafted sharp razors on her fingernails to take care of an abusive boyfriend, but she didn’t stop there.  Francis Nacho (Geo Corvera) is a Hulk-like guy thanks to super-steroids. Wendell Levi (Ric Sarabia) is a little too good with computers, and knows how to cause real damage. They were all kept under watch by SHIELD, with their powers suppressed, and that’s why they’ll go along with Cal’s plans to ruin SHIELD.

Still, they’re not as powerful as Skye, and she is now on the Gifted Index. She also has macro-molecules in her DNA that make her different. She’s set for evaluations from Dr. Andrew Garner (Blair Underwood), a psychologist who will determine how big of a threat she is. He also used to be May’s husband. Their reunion is a bit tense, especially since she hasn’t called him for a while. He does like her mom, though. Still, he’ll do this but only under his conditions, and May agrees.

Meanwhile, Morse lies to Coulson about why Hunter isn’t around. He’s really in a safe house with Mack, as they’re still trying to keep their real mission a secret. She twitches a little when Simmons says a betrayal of trust changes everything.

As for Cal, he and his crew break into Brynmore, a mental institution in Ohio because that’s where the Gifted were kept by SHIELD. He knows Coulson will be there to investigate. He said they had two inside, a creative assassin and a man with a powerful voice named David Angar (Jeff Daniel Phillips). He’s also known as the Screamer, the reason why will become apparent soon. The crew is headed to Manitowic, WI (SE of Green Bay) for a special reason.

Garner talks to Skye, and he notices she uses humor and sarcasm to hide her real fears of what she has become. She’d rather ask about their wedding and why May is called the Cavalry. He does admit he and May eloped. He also discovers Skye can cause tremors, even as she sleeps. It was really a nightmare, where she was looking though a scope during a mission, then found herself on the other side of that scope. That says it all.

Cal reveals to his crew why he wants to get SHIELD, especially Coulson. He’s still mad he didn’t get to kill Whitehall. He also revealed he conducted scientific experiments on himself after his wife died. It caused severe anger issues that even his crew is worried about.

Still, they head to the high school stadium where Angar lets out a loud roar that knocks out the cheerleaders and football players…not to mention a flock of birds flying by.

Back at the safe house, Mack offers Hunter pizza and a beer, and they talk about a past mission in Dubai. Hunter thinks it was a cover for something else, but Mack still won’t admit anything.

Morse is also careful not to reveal anything to Coulson either, but she does help him figure out where Cal is headed. Manitowic is where Coulson was born, and where his dad coached football. His plan is to confront Cal, but agrees that May should be backup. Skye also wants to help, tremors or no tremors. Since her dad is doing all of this for her, they can use that against him.

So, the stage is set for, as Cal puts it, SHIELD’s Eagles vs. his Slicing Talons. For what it’s worth, he’s got a great announcing voice.  He hopes to finally show how SHIELD isn’t as good as it claims to be. May arrives, with a gun pointed at Skye. Cal is stopped in his tracks, but he uses that as an example of how he’s right about how SHIELD treats the “Gifted”.  A confrontation is about to erupt….then Gordon, the Reader (Jamie Harris), shows up and takes Cal away.  The SHIELD crew take care of Cal’s crew, but after a lot of difficulty. Seeing her team in distress, Skye causes another tremor, but it’s really a slow rumble. She’s able to stop it, but it causes her to faint. Back at the Bus they realize it is taking a serious toll on her body, including dozens of hairline fractures in her arms. It’s because Skye hasn’t been suppressing her powers, she’s directing them inward. Dr. Garner suggests that she should leave SHIELD, something no one is willing to accept. He also says that SHIELD hasn’t changed as much as May says, maybe due to its policy of confining the “Gifted.” He reminds her of what happened in Bahrain, whatever it is. Will they have to apply that to Skye, and will that mean she’s no longer part of them? It looks that way, as Coulson and Simmons discuss this possibility. It also feeds into Simmons’ fear of people with powers. The cracks within SHIELD are getting bigger, and it has nothing to do with earthquakes.

Finally Mack takes Hunter to a place where he says is his real employer. He says it an outlier to the damage that Nick Fury left. He calls it “the real SHIELD”, complete with slightly different logo. I suspected this was coming, since we haven’t seen Edward James Olmos yet. It seems there will be a civil war within SHIELD, with a group who trusts Coulson and a group that doesn’t…or can’t. While that may seem unfair, think about it: SHIELD finds out HYDRA grew within it, Fury is dead, and they may also wonder how Coulson came back from the dead. Who wouldn’t be suspicious? This is only good news for HYDRA, and if they exploit this, they wind up as the winners.

What about Cal? He’s being kept in a room filled with furniture that he’s destroyed. Gordon is there, and Cal asks why he didn’t take Skye. Gordon says what they do is none of his concern, but they are concerned Cal’s making “too much noise, and that he is not like them, but a science experiment. So what now? Well, if Raina did tell them what happened three weeks back, it won’t look good for him. He’ll find out that just because he married an Inhuman, that doesn’t mean he’s part of their family.  It also looks like there will be also be a battle with the Inhumans and SHIELD over the fate of Skye.

By the way, while Angar and Gideon were part of this week’s SHIELD story, they’re actually featured in Marvel’s Daredevil on Netflix.

Next week, the “real SHIELD” starts plotting against Coulson,  and Ward is finally back.

Marvel’s Agents of SHIELD airs Tuesday at 9/8c  on ABC. Watch full episodes online at ABC.Go.com, On Demand (check with your local cable provider), Hulu Plus and Amazon Instant Video.