I'm responding to a lot of people here so no quotes, however...
You're asking me what the agenda of gamergate is. Well I can't really speak for it because there are tens of thousands of people involved and sure, their needs and desires differ.
I can speak for myself and say that if I had my wish websites like kotaku and polygon and ign would do the following
1) Issue an apology for their role in this whole thing. Its ok if they stay vague, honestly. Just be sorry that they played a role in this.
1b) wouldn't hurt if we saw apologies for the whole 'gaming is dead' thing. that sucked
2) Begin to start posting exclusively articles about games, the companies that make them,
and the industry.
2b) avoid posting editorials as content, avoid clickbait, avoid non-gaming related crap.
3) begin disclosing when money is exchanging hands and when favors are exchanging hands. This includes 'gifts' like tablets and pcs and free copies of games or whatever else.
3b) fully disclose all connections the author of an article has with so and so. It would be swell if you could simply click on an authors name and see things like "Owns stock in so and so" and "is best friends with so and so".
3c) at the very least when the author has a conflict of interest, to recuse themselves or disclose that information.
If we woke up on monday to every one of those sites posting letters claiming this stuff then this 'war' would be over.
Insane people would still enjoy torturing zoe quinn and probably say its because of 'gamergate' though because that's just what crazy people do.