Here we go.
Firstly, Carrington is a freak. His entire life is devoted to trying to contact aliens, and he does (the Maians). They agree to meet on Earth.
The CI got a call from Dr Carrol asking for help. Basically he wanted the CI to get him out before dD remove his personality. Jo busts him out (Def - Ext). Carrington and Dr Carrol go to his (Carrington's) Villa to discuss stuff, but dD shows up, ties up Carrington and take Dr Carrol back. Carrington mentions them hear something about their meeting in the G5 Building so he sends Jo to investigate (Chicago - G5). Jo hears their plan to kidnap/clone the president but doesn't know why. Jo takes Dr Carrol's backup personality while she's there.
Meanwhile, Carrington's alien friends call and say they were shot down over Area 51, so Jo goes there next, busts out Elvis, etc (Rescue - Escape). Then she gets on Air Force One as the stewardess so she can save the pres. The plane crashes anyway, and the pres gets kidnapped/cloned. Jo kills clone, saves pres (Air Base - Crash Site). President explains that Trent had been wanting the pres to loan him the Pelagic II (diving boat), but the pres had refused so they cloned him (so they could make the clone agree to loaning the ship). Jo and Elvis go on the Pelagic II to see what's up. The Pelagic II goes to the bottom of the Pacific Ocean, where they find the Cetan crap. Basically, it's a massive weapon that can reverse the force that holes atoms/molecules together. Activate it, and poof, Earth is gone. This weapon was created by the Skedar but they skillfully dropped it in the Pacific Ocean while they were flying over Earth. This is why they want the Pelagic II AND Dr Carrol. Dr Carrol has the power to hack it's codes and crap. Dr Carrol's personality told him it was bad, he didn't want to do it, Dr Carrol removed his personality. Understand? No? Anyway, Jo inserts Dr Carrol's backup personality (Deep Sea) and Dr Carrol decides to blow the entire place up.
This is supposed to be the end of the game. The weapon is destroyed, there's no more threat. That's why after completing Deep Sea you have "Continue" and "Replay Last Mission". There's no Abort. Har har, like people will actually follow the storyline, think there's no more missions and abort. But anyway, the Skedar invade CI. Jo saves the day, but gets knocked out at the end and captured by Skedar. She awakes on the Skedar mothership where she decides to take it over with help from Elvis. Elvis sees the Skedar home planet so they blow it to smithereens.
THE END.
PS. The Skedar needed Dr Carrol to unlock the Cetan megaweapon, so they needed dD to build it for them. They promised crazy Skedar technology in return, and Trent and Cass saw through their deceptive ways and blindly agreed. This is why Cass says the Skedar used her.
Have a nice day.
