I have a more cynical view, just brainstorming here, but maybe you'll find some of it useful. Were I to outline a book on this premise, this would be the beginning:
• Crops altered to create an addictive dependency, introduced for export to other nations. This to create a dependency on the continued exports, and thus give a severe political advantage.
• Addictive food staples produced in South America (fewer regulations, cheaper labor, experience running addictive substances across the borders) by an extremist regime with an agenda.
• Modified crops discovered and ultimately banned, but only after causing a huge upset to the political structure of today's first-world nations. Orwellian plot averted after 20+ years of slow but meaningful progress. The story begins in the aftermath of this.
• Remnants of these crops are found growing in the US. Quarantine Slash and burn squads annex huge parcels of land with little oversight to "secure it", displacing the owners, families, wildlife, entire towns...
• The effects of the crops on Wildlife are intoxicating. Deer browsing in the fields may intentionally run into on-coming traffic under the influence of psychoactive compounds in the crops, irregular migration patterns for animals, higher level predators push into human-inhabited areas in unprecedented numbers. Bears going through trash cans in the city, wolves attacking suburban pets, all to get "untainted" meals.
• Paranoia sweeps the masses. Some "purists" (a radical, back to nature faction) break off with their own political agenda and guerrilla tactics to make it happen. Think "skinny tree-hugging vegan Rambo".
• Another International group, "scientists" intend to use GM methods to reconstruct some of the tainted species and re-establish a native population that cannot cross with the tainted crops. They are funded by corporations and a corrupt government left in disarray after the collapse, so there is strife within the organization.
• Hippy Rambos fear the consequences of more genetic tampering, and begin bombing research facilities, abducting scientists, etc.
• Scientists need untainted plant samples which are currently in the possession of the hippy Rambo faction, who distributes "Purified" (Genetically non-viable) processed food to their clans from an undisclosed growing location, like a hydro-farm in an old salt mine... leading to a sub-plot where scientists, using the military and private security of their sponsors must claim samples of these plants from the other faction.
• The Hippies maintain an almost religious belief that if these crops are not cultivated anymore, nature (a praised, anthropomorphised mother figure) will remedy the plague genes in a few short generations. There may be some scientific data to back that up, but for most its held more like a prophecy.
• The problem with the hippy prophecy is that the tainted crops were addictive, people still grow them in secret where they cross-pollinate with the healthy crops. It's a drug epidemic as well. Hence the burn squads.
• Where people used to mow their lawns and spread fertilizer, suburbanites have traded in the mower for flame-throwers to burn the grass out, and traded the fertilizer for rock salt, fearing that an "Organic uncertified" plant may sprout around their homes, causing an inquiry from the burn-squads.
• Those found to be growing the tainted food are punished by tribunal, harshly. To avoid this, The colony collapse issue with the bees is encouraged by the masses to prevent cross-contamination.
• Healthy food is very expensive and tightly controlled. Tainted food that can satisfy the addictions is even more expensive and difficult to acquire. Most eat whatever they can find, as poverty is a growing problem for most people. More expensive than that are the mandatory medications to alleviate the symptoms of addiction.
• As with any faction story, there are idealists and true-believers, people using the faction to gain power, manipulators, radicals, and dissenting opinions on both sides, and all the people caught between them. Neither side is entirely correct from a logical or ethical perspective. Both are composed of people who have their own sense of ethics and align with the side that best suits their own objectives.
• Sea resources being untouched provide the majority of the food. Fish, Kelp, Shrimp etc. This shifts economic power to many small fishing islands who previously weak compared to large countries. There is fear of the Japanese Empire (the current global Super Power), built on their economic superiority as the major provider of food. They control most of the South Pacific now.
• Antarctica is a highly contested land-mass. Beneath the ice lies Oil and natural gas, and fertile soil protected from the contamination. The long days make it and ideal growing area for large scale production. In heated glass domes The Scientists work out their plan.
• The Hippies control Yellow Stone Park and other formerly protected wild-life habitats around the world where agriculture was unable to move in close enough to contaminate the region.
• Following the collapse, as information about genetic modifications was beginning to become available to the masses, Governments across the globe began changing, or "securing" the internet with the implementation of encrypted networks that replaced conventional network switching and storage devices. Only those who had completed the "approved" education were allowed access to the internet (the scientists). The rest have fallen back on short-wave radio and hard-copy books. This makes unified action among the hippies difficult. They act more like cells, independent of one another, each stronghold having it's own unique culture and power structure.
• The Japanese Empire is threatening the strong-holds of both the hippie in Australia and South Africa and the Scientists in Antarctica, as either of their solutions may pose a threat to the Japanese rise to power, as they now control the majority of the worlds food.
• The "Burn Squads" are not evil. They have a "Just Fix-it" attitude, and are specifically targeting incidents of further contamination, and those who seek to further the contamination through marketing of the contaminated crops. They are taking the "Chemotherapy" approach, kill enough of the infection to make the rest manageable. They are suspicious of Japan, and within their organization, there is a strong racial bias against anyone from South America who are blamed for starting the problems. They do however over-step their authority often, and are not empathetic to the people affected by their actions.
There's a setting for a story. Obviously needs some characters, a plot, a beginning, middle and end... But it's a start, lol. Just let your mind run down that tangent for a while, and you'll think of a million other possibilities. To Summarize:
Where would contamination come from:
I choose Colombia, as it's a huge food exporter to the world, has very little regulation, a volatile government and a fragile economy that would see some short-term gains from using GMOs.
What's the problem:
Addictive crops. Too many plot possibilities with that, and every one understands what addiction is. Explaining something like a marked decrease in available potassium in food just isn't as fun.
I know, they need a real name. People are familiar with the fanaticism some of the eco-crap creates in people. Given a legitimate global crisis, it stands to reason they would rally and have their own agenda for the world, and gain a lot of support in doing so.
If Technology can create the problem, many will turn to technology to solve the problem. As a structured and specialized education are a prerequisite to being a scientist, and labs cost money, they will be backed by those with money and power, mostly governments and large corporations.
Like knights in the dark-ages, self-assembled and organized bands of thugs given just enough authority to control the masses, but not the financial resources to compete with the leading class. This posse makes sense under the circumstances.
Of all the countries, they would likely be the first to recover, having a substantial fishing industry, relatively small (and thus easier managed) land mass for agriculture. They have a government in place that can micro-manage resources already, where as the US would have a huge cultural back-lash should a government try to do that here, even in a crisis. They have the diplomatic connections, economy, and technology required to rise to the top during these events.
The Strong-holds are a prerequisite of any substantial power. Japan, as I said can be salvaged. Antarctica makes sense if you have the finances to exploit it. The Nature preserves in the US, Africa, and Australia are very well suited to the hippies and would be uncontaminated. The Burn-squads are mobile, setting up wherever they need to be at the time, living within the chaos and trying to manage it rather than escape it.
If you borrow the faction idea, just do me one favor. For the love of God, don't do anything so cliche as having one person from each clan come together and work for the mutual good to the salvation of the planet. Better the world should burn than be saved that way.