In Minnesota, Harry Jackson is fishing with a neighbor boy. Harry offers the boy one of his special lures made out of a gum wrapper, and they talk about how the boy's grandfather is in California. Harry shows the boy a photo of his own grandson, MacGyver, and talks about how he doesn't see him very often because he's in California. Harry starts to cast, but collapses with a heart attack.
In California, MacGyver meets Pete at the Museum of Art and Natural History to arrange the transfer of a rare artifact, the Sun Boat, to Mr. Hakim with the Egyptian Consulate. MacGyver has received word about Harry's condition, but all of the flights to Minnesota are full. Hakim arrives and MacGyver notices he's wearing an amulet with Egyptian markings. Hakim explains that it's the symbol of Ka, belonging to Osiris, and that Hakim wears it as protection for one's soul. As they discuss the increasing number of black market sales of artifacts, they meet with Jeremy Stintson, the museum curator, and prepare to make the transfer. MacGyver goes to call the hospital in Minnesota. After he's left, Tarik breaks in and uses tear gas to cover his escape with the Sun Boat. MacGyver hears the noise and runs to investigate. Tarik runs to a parking garage where his car is parked. The two men struggle and Tarik throws MacGyver over the railing where he slams into a car three stories below.
As Pete accompanies MacGyver to the hospital, Hakim meets with Tarik, who is working for him as a security aide. Hakim insists that no one was supposed to get hurt, since it'll bring down more intense investigation and reveal that he's involved. If Hakim's role is found out, they'll discover he plans to smuggle out the Sun Boat under diplomatic seal. Tarik warns that MacGyver saw his face and could identify him and Hakim tells his assistant to dispose of the witness once and for all.
Hakim and Tarik go to the hospital while Dr. Brolenz tells Pete that MacGyver is suffering from brain damage and has lapsed into a coma. MacGyver is conscious of what is going on around him but unable to speak or move. He recognizes Tarik with Hakim and realizes they stole the Sun Boat, but Pete can't hear his silent warning.
Lying in bed, MacGyver sees Harry standing behind the doctors. MacGyver gets out of the bed and realizes that while his soul is free, his body is in a coma. He follows Harry out the door and discovers that he's unable to go back. Harry silently walks away and MacGyver has no choice but to follow him. He discovers himself on a dock next to a giant white ocean liner named the Osiris. MacGyver sees Harry go up the gangplank and tries to follow him. The chief purser, who introduces himself as Anubis but looks strangely like Hakim, stops MacGyver and explains that they're in the Netherworld. Only the dead can board the ship.
At the hospital, Hakim gives Tarik a syringe and tells him to inject it into MacGyver's IV.
On the dock, the crew informs MacGyver that James and Ellen MacGyver are on board the Osiris to greet Harry. Upon hearing their name, MacGyver insists on going board. The pursuer tells he clerk to check and see if MacGyver's name is on the manifest.
At the hospital, Pete checks with the police and learns that they suspect an inside man was involved. He passes the news on to Hakim, who assures him that his superior the ambassador will let the police search the consulate. In MacGyver's room, Tarik injects the syringe's contents into MacGyver's IV and slips out as he flat lines.
The clerk finds MacGyver's name on the manifest and Anubis lets him board the ship. MacGyver finds Harry, who tells him that it's not his time and he needs to get off the ship. When MacGyver points out that he fell three stories, Harry says that he still has a chance to live. They hear the second boarding call and Harry warns him that if MacGyver is still on board after the third call, he'll be trapped forever. MacGyver insists on seeing his parents one last time to tell them that he loves them and Harry agrees to take him to them.
In the hospital, the staff tries to revive MacGyver.
As Harry takes MacGyver through the ship, MacGyver says that he finally feels like he's found somewhere that he belongs. They find James and Ellen and Harry goes to give them the news. They tell him that his wife Celia couldn't make the trip but is waiting with a home cooked meal. MacGyver comes over and embraces his parents.
At the hospital, Dr. Brolenz admits that they don't know why MacGyver suddenly took a turn for the worse. Meanwhile, Hakim's man Boutros arrives and tells his superior that they've hidden the Sun Boat at the consulate. However, the police will inevitably request and receive permission to search the consulate. Hakim decides to throw them off the trail by giving them a new suspect: Pete. They'll dispose of Pete and make it appear as if he fled with the Sun Boat.
Aboard the Osiris, Ellen talks about the time MacGyver tried to fly off a garage, and James explains that even after his death, he was there to watch over them. When they say how proud they are of their son, MacGyver apologizes for the time he couldn't be there when Ellen had a stroke and died. She tells him that she understands and that it's time for him to rest. Harry insists it's not his grandson's time and that MacGyver still has people that depend on him. When MacGyver says they can get along without him, Harry tosses him a coin with the symbol of Ka and invites him to look through a ship's telescope. MacGyver sees Pete finding the Sun Boat and Hakim shooting him, and Harry warns that he's the only one who can save his friend. Rather than let his friend die, MacGyver resolves to go back. He embraces his parents one last time, and they assure him that they'll meet again. Harry takes MacGyver to the gangplank to disembark before the ship sets sail.
At the hospital, Brolenz and the nurses try to revive MacGyver, who is suffering from shock brought on by potassium. Hakim, Tarik, and Pete anxiously watch.
Anubis and his men refuse to let MacGyver leaving the boat, insisting that he's dead and won't accept it. They lock Harry and MacGyver in the engine room and prepare to cut off. As MacGyver tries to find a way out, Harry wonders why he came after him. MacGyver explains that there were issues he thought they needed to resolve, and points out how they hadn't spent much time together since refunding each other. Harry says that it's not a matter of being together on the weekends and holidays. Looking around, MacGyver sees the propeller shaft and gets an idea. He reminds Harry of the time he used the winch on their truck to pull them out of the mud. MacGyver ties a fire hose to the shaft and fastens the other end to the door. When the engines start up, the propeller shaft tightens the fire hose and pulls the engine door free.
MacGyver and Harry head for the deck and find a winch. MacGyver starts to lower himself to the pier and tells Harry to come with him. Harry tells him that it's his time and he plans to be reunited with his wife. They embrace one last time, with MacGyver calling Harry "Grandpa." Harry activates the winch and lowers his grandson down but Anubis and his men arrive and bring the line back up.
In the hospital, Brolenz tries to revive MacGyver and warns that he's not on solid ground yet.
As the line rises back up, Harry calls to MacGyver to jump. MacGyver leaps to the dock and just catches the edge. Clinging by his fingernails, MacGyver starts to lose his grip…
… And a hand reaches to grasp his: Pete's in the hospital. MacGyver is still paralyzed but manages to blink at Pete and gesture with his fingers. Pete places some powder on a tray and has MacGyver sketch out the symbol of Ka. Realizing that Hakim is responsible, Pete takes him and the others captive at gunpoint and has Brolenz call the police.
Later, Pete takes MacGyver outside in a wheelchair and tells him that the police have found the Sun Boat at the Egyptian Consulate. The Egyptians have deported Hakim and his men and they'll stand trial for the theft and attempted murder. Pete offers his condolences about Harry's death and how MacGyver couldn't make it there, and admits that he was scared at how close his friend was to dying. MacGyver tells him that he's sure that Harry knew why he couldn't make it, and that death is just a step to something else.