Here's my personal take. I have taken bits and pieces of ideas I have seen from various people and kinda amalgamated, so credit be to you guys who came up with some of this stuff.
The sequel starts off with clips and youtube vids from 2 months after the San Francisco battle. The nuclear detonation or possibly radiation leaks from Yucca Mountain caused by the female MUTO awakened a creature dubbed Anguirus near the Arizona/Nevada border. This creature instinctivlly makes its trek through areas, seeming to avoid major populated areas, but when confronted by the military it fights back viciously. These should be just clips like Cloverfield and youtube videos of the creature, because this is merely the intro. The creature makes it to SF and battles the military which lead him out to the Farallon Islands and use cadmium gas to subdue him. Then the movie switches to nightfall on the islands and around the presumably dead creature and large numbers of Chinook heliocpters heading toward his way before fading to black.
The next scene involves the new character a woman of Irish descendant (Eliza) and she leads a UN team in a ruined area. Under the screen it pops up "5 months later...North Korea" turns out that the N Koreans ahve tested three atom bombs since Sf and had an accident at one facility near the coast. This UN team was sent in to look for survivors and was allowed in because of the North's probables with....the creature that appears at the ruins of facility. It seems to be a six-legged lizard that the North has been fighting for days. The creature's appearance endangers everything and the team requests extraction. The opposite direction however, Godzilla arrives. The radiation and the creature that has appeared has lured him here. The North Korean military uses planes primarily to focus their intention on Godzilla, who swats a few down and uses his breath to bring more down. The military retreats and the two monsters battle. Godzilla wins quickly and proceeds to eat the other creature and the team is extracted.
Another month or so later, Eliza is brought to L.A. and meets with Serizawa, who was caught in Anguirus's rampage. He now wears an eyepatch over one of his eyes and is assembling an international team. The creature named Humsin that attacked North Korea seemed to originate in China, but that's not the reason he's assembling a team. The creature Shinomura that Godzilla fought years ago that was kept from the public has appeared and attacked several sites around the world and seems to be return toward Moanster Island in the south Pacific. Monarch officially moved the natives away from there in the late 50's and built a base there that was officially closed in the mid 90's. However, intelligence has indicated something may be active there. He believes Anguirus's body was not dropped into the ocean like the official story is, but it was taken there. Tensions form in this team, because of Eliza's father's history of being an IRA member and another team member that believes he was a murderous terrorist.
The group secretly goes to the island with Serizawa and finds that that there is a small fleet of destroyers from Russia and the USA there. The group stealthfully goes through the island and finds out the truth-that this Monarch facility never closed, it absorbed former Russian operatives from their own organization, and reinvented themselves as DARK ARCHON. The group is captured after tensions about Eliza's parentage cause a conflict within the group, and they find out this island is a planning ground for DARK ARCHON's new world order. This group will destabilize the world to basically create a new scientific society and has had it hands in branches of the US and Russian militaries fora long while. They even have a young woman from a neighboring island helping them. The woman, from Infant Island, named Mana is helping the group control with what she believes is her own power(it's left up to the audience to decide) and their technology to control Mothra-a giant moth that she believes is a deity (but like the original there is evidence that its a mutant and evidence that is truly mystical,, but it's left up for the audience to decide). Mothra is able to control the other creatures of the island-Anguirus, a MUTO-related creature that looks more like a smaller version of the female with back crests and an elongated beak(making it look similar, but not by much, to Gigan), and Shinomura. Mana claims that Godzilla is no better than man, because he destroyed the last natural MUTOs and wiped out their species-thus damaging the natural balance. It is also revealed the Serizawa is indeed close to 70 years old, but he in the late 80's had cancer, and Monarch produced a rare experimental cure that saved him, but slowed his aging process exponentially. So Serizawa is also responsible for disrupting the natural order. This film also explores what we do for own personal gain that alters the natural order.
Godzilla comes on land and battles Shinomura, the Mutoesque creature, and Anguirius. He promptly kills the Mutoesque creature after several minutes by biting down hard on its neck and braking it and releasing his atomic blast on the creature while his jaws are still locked on. He repeatedly injures Shinomura with his blast till the creature retreats. Anguirus's battle is mostly physical, but both creature hold back and Serizawa explains that in Alaska, seven years prior they found 64 million year old fossils of two juvenile Godzillas that were dead and preserved with a full blown Anguirus and a few fossils of young ones like Anguirus with the fossil of a female MUTO and larvae. Seems Godzilla and Anguirus's kind worked together to protect themselves from the MUTOs and explains a similar situation between a symbiotic spider and frog:
http://scienceblogs.com/tetrapodzoology ... t-spiders/Anguirus breaks free of control and seemingly sides with Godzilla. Mothra finally shows and tries to assume control of both the creatures and fails, Godzilla battles Mothra, while Eliza and her team break free and break DARK ARCHON's control of Mothra. the military on the island scrambles and leaves, while the monsters are still recovering from what had just happened. ARCHON leaves the island in droves and without its monsters they are reduced to a sizable naval force and limited a limited airforce. Mana sides with Eliza and her people and the tensions about her parentage cease, because Eliza proved herself by rescuing them all and severing ARCHON's link with Mothra. for the next few days, ARCHON launches surprise attacks on the navies of the Phillipines and Inodnesia. The technological advantage and aspect of surprise give ARCHOn a powerful advantage, then they learn how to control Shinomura directly and have the monster aid them. the group sends a message to the UN to give them a small nation like East Timor or Micronesia and demand that they are recognized as a country so they further their development of the human race. If not, more attacks from what military power they do have and Shinomura will be expected. They also tease of another secret weapon that they have. Godzilla clashes with DARK ARCHON's navy and Anguirus island hops to facilitate his travel west, while Mothra seems to be recuperating from the stress of ARCHON's control. The UN denies DARK ARCHON's threats.
Within days, Shinomura attacks Osaka and the remaining fleet arrives and clashes with Japanese SDF and American forces. Shinomura fights back against the SDF and American forces, while another new creature(add new kaiju here) arrives to aid it. DARK ARCHON revealed it was using biotech to clone/alter another one of the mutations it came across in the Pacific and has control over it by mimicking technologically Mothra's psionic control. The creatures and the force of Dark Archon puncture through the military defense and they land in osaka. Soon a figure arrives in the sky and it's Mothra. Soon Godzilla and Anguirus arrive. the monsters battle and eventually the two enemy monsters are slain and Dark Archon's forces are destroyed by the getting caught between the monsters. The monsters feel that they did what they needed to and leave. The team of Eliza and Serizawa with Mana help destroy the monster control system and watch the kaiju leave. Eliza makes a comment about Godzilla and Anguirus seemingly to be very close as Mana nods and says nature has been balanced. Then Serizawa states something that preceeds the credits, "Godzilla existed in the Perminain and the body from the Phillipines supports this idea." The group wonders why this is important. Anguirus and Godzilla coexisted 64 million years ago, and it seems the dinosaur-killing asteroid just spread radioactive material from its impact crater, awakening Godzilla's kind and mutating the ancestors of Anguirus over time. He states that Ages of Monsters are time and time again and this is the beginning of a new one possibly.
sorry for this being messing, but just kinda typed this on a break. What do ya think guys?