Ignoring all the Rasputin fanboys who still want to make the Traveler the bad guy and (despite the story from every Bungie FPS ever) the AI the good guy, let's look at the books of sorrow. The one time we have specific mention of the Traveler being around is the Hive conquest of the Ammonite (http://www.ishtar-collective.net/cards/xix-crusaders) which seems to be one of the first civilizations she empowers. The Hive annihilated them, killed the Leviathan, and [i]then[/i] the Traveler left. Of all people, the Hive would be the ones to paint the Traveler in a bad light but they don't mention the Traveler leaving like a coward at the first sign of danger, only at the point of total defeat. In this case, I guess you could argue she might have been protecting the leviathan and not the Ammonite, but lets move on to the next example we have. The Dakaua/Ecumene (http://www.ishtar-collective.net/cards/xxv-dictata-ir-dakaua) have the same caedometric paracausal weapons. The Traveler probably provided the technology too, but is not mentioned as being around or abandoning them. The Ecumene actually seem to come closer than anyone besides us to stopping the Hive (http://www.ishtar-collective.net/cards/xxvi-star-by-star-by-star) but once Oryx gets the power to "take" it's all over. (http://www.ishtar-collective.net/cards/xxvii-eat-the-sky) Again, no mention of the Traveler being there and fleeing. The Traveler tries something else with The Harmony. Before moving on, she makes the Gift Mast, a weapon containing her actual Light, and powered by a supermassive black hole, to protect them. (http://www.ishtar-collective.net/cards/xlv-id-shut-them-all-in-cells) Note that the Harmony are quite powerful and their civilization very much intact when the Traveler leaves as the Hive do not mention encountering her when they attack the gift mast. Unfortunately by this point the Hive are so strong they wipe them out anyway. (http://www.ishtar-collective.net/cards/xlvi-the-gift-mast) Presumably the Traveler learns from these mistakes and decides that simply empowering civilizations is not enough, and decides to make a stand in our system (http://www.ishtar-collective.net/cards/ghost-fragment-the-traveler-2) Whether it's due to humanity specifically or the presence of the Black Garden being in this system is unclear but I'd actually guess the latter was a bigger deal if you really want my honest opinion since that's where the real battle takes place in the collapse and Rasputin calls the Traveler "the gardener" (http://www.ishtar-collective.net/cards/ghost-fragment-mysteries) Now, I can't say exactly what happened to the Eliksni (or even when), but I think it's just the same, she seeded their civilization and then moved on to the next world to lift up. This was before, not during, the whirlwind. Think about this. Skolas is a pretty salty dude, right? Even he doesn't blame the Traveler for abandoning them or causing the whirlwind (http://www.ishtar-collective.net/cards/ghost-fragment-fallen-3) It sounds to me like the survivors of the whirlwhind figured out the Traveler was here and came in hopes that rejoining with her could restore their civilization. Only the flavor text of the Doom of Chelchis ("Where is the Great Machine?!") makes any reference that might be construed as her absence being directly related, but that statement can be interpreted multiple ways.

From what I understand from the Grimoire, here's basically how it went if everything was a single person. (Note I didn't really do the races in order) [spoiler]Traveler: Aight, I'm bout to go around the universe and ascend a bunch of civilizations. Ammonites: Ay bro can I get some of that light you got? Traveler: Ay sure bro I got chu, here's some other cool shit too. Ammonites: Aight thanks br- Oh shit the goddamn Hive found us! Traveler: Oh f*ck dat shit I'm outta here Ammonites: AW HELL NAH Leviathan: Oh shit we leavin? Aight I'm goin. Hive: Oh no you ain't! *kills Leviathan* (later) Traveler: Ay whassup I got some light, you want in? Harmony: You know it Traveler: Aight imma hook you up Harmony: Wait, tf is that? Traveler: OH SHIT DAS THE MUHFUGGIN HIVE. Aight, peace out. Harmony: WAIT WTF, BITCH BETTER GET YO FAT ASS BACK HERE Traveler: Aight hold up, I'm bout to give y'all this here Gift Mast, we good? Harmony: ... Aight, yeah we good. Hive: *starts attacking the Harmonious Fleet* Harmony: Attack! Hive: *destroys most of Harmonious Fleet* Harmony: oh shit... Hive: *topples the Gift Mast* Harmony: ALL HOPE IS LOST! *drowns themselves* (later) Traveler: Ay, who you? Eliksni: Ay we dem Eliksni Traveler: Aight here some light my bruh Eliksni: Ah sick thanks brah, I'm bout to live in peace and tranquility with dis shit ya feel me? Traveler: Yah I feel ya Hive: I don't muhfuggas, feel my wrath, ya bitch ass aliens Traveler: HAH, YEET Eliksni: WHERE DU FUQ MY ***** GO?! Chelchis: Ay bruh it's all cool I got this Oryx: *shows up* Chelchis: Aw shit, we dead (later) Traveler: Psst... psst! Humanity: Woah! What are you? Traveler: I'm a god, bitch, now you want the good shit or naw? Humanity: Aw hell yeah Traveler: Aight there ya go Humanity: Aight sweet Darkness: HAHAW HELL NAH TRAVELER, WE FOUND YOUR ASS Traveler: DAMMIT Humanity: AAAAAAAAAAAAHHHHHHHHHH Traveler: WHY DOES THIS KEEP- nah, you know what? I'm f*cking outta here. Rasputin: *holds up gun on Traveler* you ain't goin anywhere, pansy ass bitch Traveler: Aw, f*ck you! Shit well I'll guess I'll just hang here and slowly try to regain my Light[/spoiler]

From the description of the Kings fall weapon Doom of Chelchis I believe it was because the Hive were coming.

The traveler is a little bitch and as soon as it sees even the slightest bit of danger it dips out. That's why Rasputin damaged it to make it stay on earth and actually grow some back bone instead of leaving. It's philosophy is to preserve life no matter what, even if that means abandoning a whole race.

From what I understood the fallen tried to pump their ether into the traveler

We are like power rangers. Think about it. Traveler = guy in blue crystal thing.

In short, she was scared and ran until she met us. When the darkness came she "stood" and fought. [spoiler] either the darkness or Rasputin -blam!-ed her up, or both. We don't really know.[/spoiler]

They cut off their arms. I'd leave them too.

Maybe because it started to realize the fallen were starting to abusing the power and we're becoming evil. Maybe the Darkness was coming; so it fled for its own survival but ended up abandoning the fallen at the same time.