
These issues are the “Wake the Beast” storyline, which focuses on the threat of the Leviathan organization. As with most Jonathan Hickman stories, it’s complex and layered, and hard to summarize (and also, of course, well worth reading). Nevertheless, I’ll try to write about it…
Leviathan is basically Russia’s answer to SHIELD…Or maybe a better analogy is Hydra, because Leviathan tends more to the evil side. They’re at war with Hydra, in fact, and they need to awaken their leader, Orion.

Leviathan agents attack Silver Samurai and Clan Yashida to recover a “box” that we later learn contains a source of power that can revive Orion.
There’s a lot of history here, and it’s revealed through intermittent flashbacks. We see that six years ago, Kraken (of Hydra) first met Gorgon and gave him a sword named “Godkiller.” At the same time, Hydra created the relatively new character Hive. Years later, Kraken is killed by Jake Fury. This means the current “Kraken” is a different dude–none other than Jacob Fury himself, taking the role of the man he killed.
And speaking of Fury’s relatives, he introduces Quake to the “black” and “gray” teams that he’s also running–which includes Nick’s son, Mikel.

Fury also makes an adjustment to the Secret Warriors team, firing Sebastian Druid via a “dear John” kinda letter.

Quake confronts Fury about his having kicked Druid off the team.

It’s cool how Quake develops across this series, turning from a naive child into a leader.
Leviathan kidnaps Viper, in what is clearly an “inside job.” This alerts Baron Von Strucker and Gorgon that there’s someone betraying them from within. We the readers know that Contessa Valentina de Allegra Fontaine has been posing as Madame Hydra, while secretly working for Leviathan. Through a flashback, we get her motivation: She was recruited by the organization as a child, after her parents were killed, and then was recruited by Dum Dum to join SHIELD. So, she’s been a double-agent all along. This is a fully believable retcon, by the way, given how she’s switched sides many times across her history.

Fury and Contessa have a conversation where Fury reveals that he now knows that she’s a spy–which of course makes him sad because the two have been romantically linked in the past. Hickman tries to show how this betrayal drives Nick Fury inward, making him trust people less but…It’s really not much of a transformation. Fury has NEVER trusted ANYONE.
There’s another spy, too: Hellfire is shown talking with Strucker, making a deal that he will betray Fury if Hydra will protect his girlfriend, Quake.

Strucker has gotten a cool upgrade. He has a giant fire fist.
At this point, Leviathan have what they need to resurrect Orion, who is being kept in a … tube, of course!

It’s Marvel’s favorite way to store characters (see tag below).

Hydra tries to stop the resurrection but arrive too late, finding only Contessa, dead–shot to death by Viper.

But since death means nothing to these people, Hydra revive her as the new Madame Hydra.

Another side plot shows Yo-Yo and Stonewall road tripping to meet their parents, which offers a reunion between Stonewall and Absorbing Man.

Creel is often portrayed as a “chaotic good” type these days, but here he is a stone cold villain.

Issue #16 is kind of a wrap up, taking place two weeks after all of the above events. It offers more of the original Kraken’s back story, but mainly shows Leviathan and Hydra attempting to negotiate a peace–but when Strucker refuses to bow to Orion, it all ends in a big fight. With both teams weakened from the battle, Fury tells his teams that it’s time for them to proactively strike.
There’s tons of subplots and lots (LOTS) of exposition, so only careful readers will find this a rewarding chapter.