Have Vita OS with FO3 GOTY edition, patched to 1.7 with all DLC's and 100+ mods managed with FOMM (B.Steel loading order is #1, just after Fallout3.esm). Broken Steel items and monsters are present in game, but after starting purifier (or having S.Lyons do it), B.Steel plotline does not activate and game ends.

Have previously activated and played B.Steel quests with mostly same mod setup, but for some reason current character gets only game over after starting purifier.

Any ideas on how to get B.Steel plot to activate?

Are you using a custom race? If so, you'll need Custom Race Ending Broken Steel Override from Nexus.

No. Just a standard human male character.
My suspicion is a mod conflict, possibly the "Amata Follower" mod.

I'll try a reload and bring Fawkes, and see if I get the Broken Steel specific dialogue options at the purifier.
Any other ideas in the meantime?

Just reloaded, and successfully sent Fawkes in. But after the final cut-scenes, the credits roll..and game over. If memory serves, when B.Steel main quest properly starts, final purifier cut-scene transfers to waking up in the Citadel, without game credits being played.

Yeah, you should see the ending and then wake up. Please post your load order.