The film continues the storyline of the film Daredevil where in Elektra was killed by Bullseye. The story is introduced by a man's voice (later revealed to be the martial arts master Stick) explaining that there is an ancient war being fought between good and evil. The evil is introduced as a group called The Hand, whilst the good follow Kimagure, a martial art that supposedly makes its practitioners able to foresee the future and control life and death.


The next scene introduces Elektra dispatching a squad of bodyguards and assassinating of a character named DeMarco. DeMarco is sitting in a larger armchair resigned to his fate and is killed by Elektra throwing one of her Sai into the back of the chair and through him. It is later revealed that the dead Elektra was revived by Stick. For a while she was trained as his student, but soon she is asked to leave; thus beginning her life as an assassin.


Elektra receives an assignment to assassinate Mark Miller (Goran Višnjić), and his 13-year-old daughter, Abby. As part of the contract, she is required to stay for some days on their island refuge before the targets are revealed. In this time she unknowingly meets and befriends the two people she has been hired to kill. When told Mark and Abby are the targets, her feelings for them leave her unable to kill them and goes to leave the island, in the process noticing two new assassins. Instead of leaving the island, Elektra returns to Mark and Abby's house and kills the two newcomers, in the process discovering they have been sent by The Hand.


Under the misapprehension it is Mark that The Hand wish dead, she leads the pair to Stick (Terence Stamp), as he is apparently leading the fight against The Hand. In a pool club, she confronts Stick by trying to grab his throat, but he grabs hers and slams her onto a pool table. He then tells her she has not changed since she left his tutorship. Elektra also discovers Mark knows why The Hand is following them, although viewers do not learn the reason at this point.


After the failure of the two Hand assassins, the leader of the group gives the task of capturing the "Treasure" to his son Kirigi and his fellow warriors.


Elektra leaves the pool club in anger and is followed by Abby and Mark. Noticing an eagle appearing out of graffiti art on a wall, she realises The Hand has found them and decides to help the pair again. She drives them to the house of McCabe, her negotiating agent. In the form of a bird Kirigi follows them to the house and after killing McCabe, hunts down the trio in the forest. Elektra kills Stone tricking him into breaking down a large tree, crushing him. Abby and Mark kill Kinkou with one of his own daggers. Elektra discovers Abby has martial arts skills. Distracted by this knowledge, Elektra is attacked by Typhoid, who gives her the poisonous Kiss of Death. Abby attempts to intervene, but is stopped by Kirigi.