Here's some of my theories for right now.
I think the real villain all along is going to be Gambi. I think he been playing both sides of the fence for his own personal game and Jefferson is beginning to catch on to him. I think the only reason why Gambi originally was urgent for Jefferson to return as Black Lightning is so Black Lightning can weaken the 100 Gang in which in turn would give Lady Eve and/or the Shadow Board to take Tobias out. I think the main reason why Gambi didn't want Black Lightning to kill Tobias is because he still have any agreement with Lady Eve and if word his involvement or relation with Black Lightning caught wind then it would be his ass.
Keep in mind, it was Gambi that put in Lady Eve's ear about Tobias' right hand and killing him. He knew Tobias would retaliate. He also knew that Black Lightning was set to kill Tobias, but he want Lady Eve and Tobias to cancel each other out. That way, Gambi would have complete control and continue to use Black Lightning as a pawn.
I also think, like in the comics, that Gambi is the one responsible in the death of Jefferson's pops, but it was made to LOOK like Tobias did it. You notice in the flashbacks (both times) it showed Tobias' goons only KNOCKING HIM OUT, not exactly killing him. I think that'll be the biggest twist that it was really Gambi that did it and he kept it a secret the whole time.
I also think that Tobias was resurrected 9 years ago when everyone thought he was dead. If La La is able to resurrect, and we know that Tobias doesn't age, I think that Tobias was resurrected too and went into hiding. That's a longshot theory, but since people being resurrected through Lady Eve is not introduced officially, it is a strong possibility. And if that is the case, it is the reason why Gambi and Lady Eve made an agreement of who's off limits.
But who knows what really happened or will happen. All I know is that all eyes is on GAMBI. Whatever that happened or is happening, Gambi's fingerprints are all over it.