Continuity mistake: When Craig first discovers the portal door his crouching position changes slightly between the camera shot inside the tunnel and that from the office, and again when he closes the office door and goes back to the portal door.
Lester(Orsen Bean), the owner of the office building, found the portal into Malkovich.His plan is to go into Malkovich with a large number of elderly people, taking them all into Malkovich's younger body which saves them from death and he decided to let Lotte(Cameron Diaz),too.But she tells Lester that his husband Craig (John Cusack)has taken control of Malkovich like his puppets.Meanwhile,Craig controls Malkovich so that the pregnant Maxine(Catherine Keener)can like him.Few months later Malkovich/Craig becomes the greatest puppeteer,but Maxine starts missing Lotte and goes to Lester and Lotte.Lester,pretends that he had kidnapped her to trick Craig into leaving Malkovich though he decided to stay in fear that Maxine won't like him anymore.Lotte becomes enraged at Maxine for leaving and tries to kill her with a gun.Maxine hesitates and runs inside the Malkovich portal and Lotte chases her.Because of Craig controlling Malkovich they wind up in Malkovich's subconscience instead of his mind.As they go through Malkovich's memories they wind up in Malkovich's childhood on a bus.Maxine,hides behind a seat and jumps at Lotte as they fall out of the bus and into New Jersey turnpike.Maxine tells Lotte that the baby is also hers and they become happy.Meanwhile,Malkovich/Craig goes to a bar and has a fight and realizes that he is not Malkovich then calls Lester he will leave.As he is thrown out into the New Jersey turnpike he sees Maxine and Lotte together.As elder people go inside Malkovic and as Lester tries to wait for Lotte though there is no time and he goes in Malkovich while he is still ripe and Malkovich controlled again,but this time by Lester.As Maxine And Lotte get hitchicked by a car,Craig as himself shouts at Maxine that he will enter back Malkovich so she can love him again.Craig,entersafter Malkovich isn't ripe.7 years later. Malkovich/Lester and the elderlys invites Charlie Sheen to his house and it shows Malkovich/Lester is living with Lester's assistant,Floris(Mary Kay Place).Malkovich/Lester tells Charlie that they can live forever by entering,Emily Malkovich,Lotteand Maxine's daughter.And we see Emily with Maxineand Lotte at a public swimming pool.As Craig,whoentered Malkovich too late is trapped in Emily controless.As he keeps repeating "look away" from Maxine as Emily stares at Maxine and Lotte unaware of everything.
Maxine: Here's the thing: If you ever get me, you wouldn't have a clue what to do with me.
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