Note: There will be spoilers in our summary.
Recap
Last episode the Bus was surrounded by HYDRA planes. Ward leaves with Skye and Raina. May tells the others to strap in as she does some fancy maneuvering in the Bus. Being chased by HYDRA planes, she dives the Bus into some heavy clouds, ejects some pods, and pulls up, cloaking the Bus at the same time. The ejected items were hit by missiles. They land and pick up Coulson. He figures Ward is taking Skye to her father. They haven't given up on Mac but they need to stop HYDRA from entering the city first. Simmons is talking to Fitz and he tells her not to act like Mac is still alive just because he was his friend. She points out that since they're dealing with alien tech, they don't know what the city is doing to him. It could've taken him to control him. Hunter tries making Bobbi feel better about the possibility that Mac is dead.
May is frustrated she didn't shoot Ward. Coulson says she did the right thing. The rest of their team is still alive. Skye can take care of herself. She's turned her into quite the agent.

Ward brings Skye to meet her father. He compares the way she carries herself to, presumedly her mother. He introduces himself as Cal*. Skye doesn't take his welcome too well since she was kidnapped off a plane. He admits he's nervous while Skye remains cold. She says he's a monster and a killer. He says it's because his little girl was stolen from him. He explains he wasn't always like this. She was born in China and her mother was Chinese. He worked in a clinic and people liked him. He apologizes for not being there or protecting her. He wasn't there before but he's there now for what's about to happen. He says he wants to help her so she tells him to help her out of there. He says he can't because this is her destiny.
Skye is outraged at the idea that her destiny is it be locked up with him with HYDRA. She says he's a bad guy since he's working with Whitehall and HYDRA. He says not a bad guy! Her mother had a gift. She came from a line of people with a gift. She has it too. She can transform. She worked at the clinic. A group of men came into the clinic. He says SHIELD came in and took her. She was dangerous. She was take. To Europe but it was too late. Whitehall cut her to pieces and took her organs and dumped her body. He starts humming. She says she heard gat before. She used to sing that to him as a baby. Whitehall sends someone to talk to her dad. He says now that he's served his purpose, he's going to kill Whitehall.

Simmons says hazmat suits should work. Coulson tells Koenig that if things go back, initiate the protocols. HYDRA is trying to drill into the city. Whitehall talks to Skye's dad, Ward, and Raina. They bring in Skye and he orders he to touch the Obelisk. It starts to light up and she uses it on a guard. They're still unarmed. Whitehall figures out who her mother was. Skye's dad is knocked out. Ward is to be monitored.
Coulson, May, Hunter, and Bobbi set out to find Skye. Simmons, Fitz, and Trip go to head into the shaft and plant some bombs. Trip heads down. Mac isn't there.
Ward is handcuffed and Agent 33 is watching him. Skye's dad wakes up and Whitehall has a device to stop him. Whitehall wonders what Skye's gift must be. He's going to experiment in her and make her father watch. Skye's dad breaks free and kills a guard watching Ward. He sets off on his own to kill Whitehall.
Whitehall is about to shoot Skye's dad but Coulson shoots him from behind. He's outraged hat his vengeance was taken from him. Agent 33 comes and starts shooting. Ward gets out and frees Skye. As he checks the door, she grabs the guards gun a d shoots Ward a few times. She finds her father beating on Coulson. She yells out "Dad!" to get him to stop. She says she won't go and transform. She tells him to leave. He says he'll be waiting and he'll always love her. He leaves and calls her Daisy.**

Agent 33 finds Ward and doesn't know what to do. Ward says he can get the, out of there she helps him. Skye tries to get the Obelisk but it's gone. Raina took it and is entering the city. She finds Mac, in a hypnotized-type state, and tells him to take her there. Coulson says he has to go after Skye before the bombs go off. He tells May to get everyone on he Bus. Trip heads back down the shaft to disarm the bombs and find Coulson and Skye, without a hazmat suit.
Skye finds Mac and he doesn't respond. She keeps going after Raina. Raina stands as the Obelisk starts to react. The chamber starts closing. Trip made it in but Coulson is outside. The Obelisk is changing into crystals. Mist shoots out. Skye and Raina apparently turn to stone. Trip kicks the crystal. Skye and Raina apparently turned to stone. When Trip kicked the crystal, pieces of the Obelisk stabbed him. He falls and turns to stone himself. Skye starts moving and comes off of her cocoon. Raina's eyes have changed and she has some spikes on her face. Mac seems okay but Trip is dead as the whole places starts to shake.
There's a glowing box. Inside is another Obelisk. Someone*** unseen talks on the phone, "There's someone new. Tell the others I'm on it." The man speaking has no eyes.
Thoughts

You could feel the suspense building throughout the episode. The opening scene with the Bus being chased by HYDRA was a little cliché but it added to the action.

In continuing to shake things up, we still have different levels of good and bad guys. Ward has made it clear here he's not necessarily loyal to HYDRA. He was loyal to Garrett, who unfortunately went crazy. As Raina put it, he's doing what he's doing (bringing Skye to her father) because he's in love with her. There's obviously no way, at this point, she's going to forgive him for betraying them. She did shoot Ward several times. Then again, because she's shown a huge leap in her training, she could have easily killed him if she wanted.
With Whitehall seemingly dead, there's a bit of a void in terms of bad guys. HYDRA still exists but who's in charge now? We know, from Captain America: The Winter Soldier, and mentioned here, Baron von Strucker is around somewhere. Ward leaving with Agent 33 leaves the door open for them to still be a thorn in SHIELD's side.
Is Koenig an LMD or was did we just get another joke/tease?
*Who is Skye's father? He said his name was Cal. Many have been theorizing that Skye's father is really...Calvin Zabo, aka Mr. Hyde.
**Who is Skye? If Skye's dad is Mr. Hyde and because he calls her Daisy, that means Skye is really Daisy Johnson. It seems the Obelisk turned into a Terrigen crystal. We then saw the Terrigen Mists unleashed upon Skye and Raina. They went into cocoons and were transformed. So apparently Skye is really Daisy and an Inhuman? This changes her origin from the comics but the Cinematic Universe is not the same place as the comics.
The big question is, how is Marvel going to handle Skye in the S.H.I.E.L.D. comic that Mark Waid will be writing? But on the cover, we see Coulson, May, Fitz, and possibly Simmons. Perhaps Skye won't be in the series since she already exists in the comic universe as Daisy. Skye's origin, as Daisy, here is clearly different from the comics. It's a matter of how much cohesion Marvel wants in their comics and Cinematic Universe.
***Was the guy at the end Reader from INHUMAN?
This was a great episode for the mid-season finale. The scene with Skye's transformation was something. It's going to be a long wait until March.