It is explained in D3, yeah.
In D2, the soulstones are destroyed, but that's not equivalent to destroying their souls, rather the idea was that it sent them back to the Black Abyss (I believe this is actually stated in D2, even), where demons originally came from (but you will note that they managed to get out of that before). This essentially equivalent to Batman dusting his hands off after slamming the Joker in a cell in Arkham Asylum and saying "Well I never have to worry about that guy again!", when he full-well knows the Joker has escaped Arkham before!
But specifically in D3, the Evils left "traces" - i.e. corruption - on Sanctuary, and Adria used this to essentially pull them into the Black Soulstone (which was a major thing in D3). The soulstone when was used to create like, powered-up super-Diablo out of Leah (nobody liked this plot development at all, I note). This Diablo was defeated and shoved back into the (overloaded, somewhat unstable) Black Soulstone which was then put in a "safe place" (lol as if) by the Horadrim.
Malthael (the Angel of Death) then immediately stole (killing most of the people protecting it, in an admittedly cool cutscene) the Black Soulstone to try and drain the souls (or part of the souls - enough to kill them) out of all humans in Sanctuary (basically just taking the "Judge Death" approach, I feel like that's probably where they got this from), and stopping him doing this is the plot of the D3 expansion. He then got mad when this failed and shattered it, and long story short this broke all the Evils out again, though as of D4, certainly Ba'al and Diablo are still MIA.
On the direct contrary he is the main (indeed kinda only) good guy in D3. Other angels are terribly naughty though.