'Shadowhunters' spoilers show something worse is coming after Jonathan's unpleasant reunion with Lilith

Nothing good could ever come out of summoning the evil queen of Edom, and Clary Fray learns it the hard way on 'Shadowhunters' season 3, episode 16 'Stay with Me.' Ever since the mid-season premiered back in February, we have seen how Clary (Katherine McNamara) has been bound to her newly resurrected evil twin, Jonathan Morgenstern (Luke Baines), due to the life-force rune that was etched on the two of them by Lilith (Anna Hopkins), the evil queen.

But the new episode finds Clary bearing the brunt of summoning Lilith to get rid of her rune, as her plan backfires and ends up resulting in Jonathan reuniting with Lilith, who also happens to be his mother. But as sinister as this development sounds, there are worse things yet to come.

So far, we have known Jonathan as the angry, evil brother of Clary, who wants her to join him in the dark side. And while Clary's life-force rune that connects her to him portrays its bursts of darkness every now and then, we have seen the redhead strategize and skillfully evade Jonathan's traps. So, naturally, Jonathan continues with his next agenda on his evil to-do list, and that is to secure the Morningstar Sword that would give him additional powers. 

In his pursuit of the sword, Jonathan goes to meet the Seelie Queen, who promises him the object of his desire, in return for Lilith's life. That's right, Jonathan has been asked to kill his mother, and the woman who resurrected him to a new life, in exchange for what he truly wants. It is at this moment that we get a clear picture of just how powerful Jonathan's inherent darkness is.

Unflinchingly and with heavy conviction, he promises the Seelie Queen Lilith's life in exchange for the sword and embarks on the journey to kill his mother. Until now, as a viewer, it wasn't hard to deduce that eventually, Jonathan would reunite with Lilith, and thus the two would unleash their own forms of hell on the shadowhunters; but things are different now.

With this simple promise, Jonathan has proven he definitely does not care about family ties when it comes to achieving his ambitious desires, and if he is ready to erase his own mother on his path to what he believes is greatness, killing off his twin doesn't seem like an impossible thing for him either. Meaning, Clary's life is in even graver danger than it was at the beginning of season 3B.

So, here's what happens: Jonathan tries to kill Lilith - the all-powerful evil queen - who doesn't have a hard time slipping past his murderous advances even though she has been confined by Magnus Bane's (Harry Shum Jr.) magic. But things get even messier when Clary and her friends set out to force Lilith to remove the life-force rune from her body, as even the Malachi Configuration isn't able to keep them from the dark force that is Lilith.

Why? Because at one point in the face-off between Clary and Lilith, Jonathan decides to make a surprise appearance, thus changing the game for the shadowhunters. A brutal, but exceptionally bad**s fight scene ensues with Jace Herondale (Dominic Sherwood) and Izzy Lightwood (Emeraude Toubia) taking the forefront, the two of them fighting together against Jonathan, but in all of this, they tend to forget that Lilith is still very much present there.

Using this distraction to her advantage, Lilith manages to seduce Cain into freeing her from the magical entrapment, and yes, this is the Cain from the Mark of Cain which was the root of Clary and Jonathan's connection as we have witnessed this season. As a brief silver lining, Clary is able to transfer Jonathan through a portal, into the shadowhunters' institute's brig, but there's no overlooking the burning issues at hand.

At the end of episode 16, new danger fronts the shadowhunters as Lilith is free. And even though Jonathan might be trapped, there's no denying that it will be only momentarily. There's a high chance that Lilith might free him, or worse - might come back to take his life for his blatant deceit. But we all know that with Lilith around, there's no hope for even a vaguely happy ending for anyone, let alone the shadowhunters.

'Shadowhunters' returns with episode 17 'Heavenly Fire' Monday, April 8, at 8/7c, only on Freeform.