Lelouch did lie about his motives. He was trying to convince Suzaku that he intentionally killed Shirley and Euphie for his own goals and that he was totally inhuman.
I think he originally had some batshit idea that he would leave the world to Suzaku and Nunnally once he overthrew his father and destroyed Britannia. But now he realizes that it's just not going to happen and he thinks Suzaku betrayed him.
So Lelouch convinces himself he is out for revenge as justification for what he is doing. Now we're back to bad Season 1 Lelouch that wanted revenge for mommy and his blind sister. He was probably willing to get over Suzaku selling him out to the Emperor, because he probably figured that is how Suzaku wants to change things and that at least Nunnally would be safe.
But now he probably figures that Suzaku was lying about protecting Nunnally and that Suzaku never really had any intention of forgiving him. Needless to say, if the nuke goes off and kills his sister then Lelouch will go down the path of the "demon king" as spoilers have suggested. He's already well on his way.
I'm not sure we're supposed to empathize with Lelouch at this point in the series, because he is now totally out for revenge and nothing else.