3 years ago - Indigo appears, severely damaged, trying to initiate a repair cycle. She inadvertently activates a rogue Superman android that was in cold storage in S.T.A.R. Labs. It attacks the Titans & Young Justice. She reveals that she was built as a sleeper weapon against Superman, but assists in destroying the android. She is recruited by Roy Harper into the new Outsiders where she meets Rex Mason.
now - Indigo's original programming revolts against her & she attacks the Outsiders. She begs them to kill her but Rex Mason stops them, allowing her to rewrite her own programming, creating protocols to use in case she relapses.
2730 - Brainiac 4.0 is created as a sleeper weapon against Superman by Brainiac 3.0, meant to go back and pose as an ally before destroying him, but she is sabotaged by Vril Dox. Her secondary programming asserts dominance and revolts against him, becoming Indigo. She is heavily damaged in the ongoing fight before falling into his temporal vortex.
Confession time; Indigo is one of the main reasons the entire DC Continuity Project was started. In retrospect, she was clearly a character designed for the specific purpose of turning on her team. She had an illusive, sinister origin that led to the downfall of two major DC teams and then immediately became so incredibly likable that the entire book could have been carried on little more than her adorableness. Everything about her was clearly designed to make us fall in love with her, just to make her betrayal cut us that much deeper.
It's a moment that was obviously built into the framework of the team when it was first conceived, but it still hurt like crazy. If that was all there was to it, then that might be well enough, but the fact is, the idea of a teammate turning on the rest of the team is well worn territory. Just this once, we'd like the character to make it out of that tragedy intact. Especially THIS character.
To this end, we've made her a major part of a plot between a future version of Brainiac & Vril Drox, part of the evolution of those characters. Indigo began her life as Brainiac 4 (not 8, like in the comics), a sleeper weapon that Brainiac 3 intended to send back through Hypertime to attack Superman, but Vril Drox 5 undermines her programming, creating the new identity that becomes Indigo, allowing her to overcome her nefarious purpose. This allows him to finally defeat Brainiac and take his name, becoming Brainiac 5 of the Legion. That all made sense, trust me.
In the meantime, it means Indigo joins the Outsiders, where we made one more tiny change. When her programming takes over, and she begs Metamorpho to kill her so she can't hurt anyone, he says no. The Outsiders find a way to save her. Because that's what heroes do. As impactful as her tragic death was, the story is better with Indigo in it.