Yeah, Tom is dead. Really dead! They gave Ryan a going away party with cake, so if we see Tom again, it'll be in flashbacks.
They had to "reset" the show, Sherree. It's now back to about mid-way through the first season. Keeping Tom alive (He was supposed to die in the pilot) and Megan Boone's actual pregnancy both significantly altered the original story arcs. I believe that the writers are trying to get back to the original idea.
Depending on which blogs you read, it's highly likely that the current Raymond Reddington is an imposter, a construct of one of the intelligence agencies, and that he was one of the Russians raised to become an Amercan. That idea was explored in the 2nd or 3rd episode of "Blacklist Redemption," which is worth watching some rainy weekend if you missed it.
The bones are likely those of the original Raymond Reddington, who may or may not have been killed by Katerina Rostova (Liz/Misha's mother).
Liz/Misha may be the original Raymond Reddington's daughter, or she may be the imposter's daughter, or she might even be a clone from the Russian Warrior Gene Program (some blogs speculate that is Tom's true origin, plus he may be Liz/Misha's brother/half-brother/cousin). I don't buy that!
In any case, the plot got too dang convoluted, so I don't mind a re-set at all, especially if the writers will go back and clean up some of the loose ends that got lost in all of the clutter.
If you've never re-watched the pilot or the first season, go back for a re-watch and you'll see how much the story arcs changed.
I used to be a lot more active on several of the Blacklist boards, but I got fed up with all of the convoluted plot twists and things that were never resolved. I almost quit watching, but it is about the best things on TV these days.
It's the only show I'm watching on network TV. I have a ton of other things to do.