Unresolved mysteries
This movie has some great plot twists and some unanswered secrets which are never fully revealed so I'm going to try and address these best I can for those who are confused by this movie. Feel free to correct me if you think I'm wrong about anything.
Who is Curtis Mahoney and who is his employer?
It is never directly revealed who Curtis Mahoney's employer is but it's clearly implied that he is working for the government. Most likely he is an independent investigator who was originally contracted by the government to investigate the Franklin Foundation due to it's suspicious financial activity and possible crime ties. Mahoney was likely investigating the Foundation for a long period of time before infiltrating Dr. Terrell's research facility since he was easily able to blackmail Harold DeMilo by threatening to unveil some damaging secrets like Demilo's homosexuality and David's ties to the company.
In an early scene Mary Ann is working night shift in the control room at Alpha's tank and notices somebody trying to open the locked door. She then gets on the intercom and alerts Jake and Maggie. Who was trying to gain access to the facility?
This is also never revealed but most likely it was Curtis Mahoney since he was on the island at that time. It was obvious already that Mahoney was not a freelance reporter as he claimed to be but actually an investigator trying to uncover Dr. Terrell's secret research. However, it is also possible that a member of the foundation might have snuck onto the island that night and wanted to access Alpha's records but this is unlikely. The foundation was already aware of what was going on at the facility since they had one of their members "David" working on the inside. Also, prior to that scene Harold Demilo visited the island and Dr. Terrell showed Harold the secret audio recordings of Alpha talking in that room.
What was David's connection to the Franklin Foundation? Was he aware of what the Foundation had planned?
Late in the movie David received a strange phone call from someone claiming to be Jake, ordering him to remove Alpha and Bata from their tank and load them onto the yacht. However, despite what this scene implies, David was not "tricked" into taking part of the conspiracy. He was in fact employed by the Foundation all along and was well aware of the plan. This is clearly revealed by Mahoney. After Alpha and Beta are kidnapped by David and the Franklin Foundation, Curtis Mahoney revealed some disturbing secrets about David. David was in fact an ex convict living under an alias. His real name was William Konklin and he was a former US Navy EOD who was stationed in San Diego. During his service he was arrested for trying to smuggle heroin across the border. Following his arrest he was sentenced to military confinement but the Franklin Foundation was able to get him released due to their government influence in exchange for him working for them. The foundation felt his skills in handling explosives would be useful in carrying out their plan. David was also responsible for planting bugs in the intercom system at Jake and Maggie's house since he was the one who installed them.
Who killed Curtis Mahoney's partner Stone?
During the night before the dolphins are kidnapped, Stone goes against Curtis's orders and infiltrates Dr. Terrell's research facility. There he is shot by an unknown contact and later discovered dead in the pool. It is revealed that Alpha's records and audio recordings were stolen from the control room. Most likely, members of the foundation were also at the facility that night to steal Alpha's records, noticed Stone, and killed him to prevent him from discovering their plan. It is also possible that David acted alone and killed him since he was the only staff member who was aware of the Foundations evil plans for the next day.
Why did the Franklin Foundation send a plane to the island at the end of the film? Why did Curtis Mahoney tell everyone they had to leave?
After Alpha and Beta destroy the yacht, killing David and his co conspirators, we see Harold Demilo in his office shredding papers given to him by his secretary. This implies that Harold Demilo learned that the plan to destroy the President's boat was a failure and felt the only thing left to do was to destroy all the evidence of the conspiracy before authorities could find out. This includes the dolphins. Knowing that the Foundation was likely not going to let the dolphins live, Jake and Maggie knew the only way to save them was to release them into the ocean.
What happened to Jake, Maggie and the rest of the staff at the research center? Did the Foundation want to kill them as well since they knew their plot?
Most likely they are fine. Before Alpha and Beta returned to the island, Dr. Terrell already decided to shut down his operation upon finding out that his research was being used for evil purposes. He had all the records destroyed, the tanks were drained, and he had all the other dolphins released. There was also no way he or even Curtis Mahoney could prove the Franklin Foundation was involved in a plot to assassinate the president using the dolphins. Shortly before the aircraft landed at the facility at the end of the film, Alpha and Beta are told to go out to sea and avoid humans while Jake, Maggie and the rest of the staff fled the facility and into the island. All the foundation found was an abandoned facility with all the dolphins gone and the records destroyed.