Shinji reach the city and was received by Misato Katsuragi. At the same time, the third Angel, named Sachiel was on its way to create havoc in the city. when the 3rd Angel begin to attack the city, the United Nations counter-attack with conventional weapons but failed. All operations to eliminate the Angels was then handed to the special UN organization called NERV commanded by Gendou Ikari.
After NERV was given full authority to launch the counter-attack, they sent the only weapon that can defeat the Angels, the Evangelion Robot Eva-01, piloted by the son of Gendou, Shinji Ikari. Despite Shinji's protest to pilot the robot, he was forced to ride it due to the desperate situation and with zero experience except the uncanny ability to blend with the psyche of the robot, he went into action.

episode 2
The Beast

After defeating the 3rd Angel, Shinji was hospitalized due to the stress brought about by the unexpected turn of events that happened so suddenly during the fight with the Angel, in this episode, Eva-01 unexpectedly went out of control, rampaged and heavily injured the Angel that prompted the Angel to self-destruct. After recovering from the shock of riding Eva-01, Shinji was transferred under the care of the head of strategic and tactical command: Misato Katsuragi, and was forced to stay with her in her condominium, under her direct supervision.

episode 3
A Transfer

Its been two weeks since Shinji's life completely changed and after transferring to his new junior highschool, he has not gotten used to his new life. Being the introvert he is, he wasnt able to make new friends at school, in fact when it was known that he was the pilot of the robot who rampaged around Tokyo-03, a classmate named Touji, whose younger sister was gravely injured in that incident, bullied him after class, and it was this time when the 4th Angel attacked. After barely less than 5 minutes of internal power after the Eva-01 electrical cable was disconnected, Shinji went for a suicide attack that defeated the angel before his power run out.

episode 4
Hedgehog's Dilemma

Shinji hated to ride the Eva-01 in the first place and finally got the courage to run away from everything, from Misato, from Nerv, from his classmates and from Eva-01. But with nowhere to go, he spent the whole 2 days riding a loop train, sleeping in a cinema and walking in the field outside Tokyo-3. It was here that he met Kensuke, one of his classmates who was camping out,they camped that night and the following morning the intelligence section of Nerv got hold of Shinji's location and took him away. After Misato confronted him about his intentions and feelings about his new responsibilities as an Eva-01 pilot, she got infuriated by his cold response and dismissed him from active duty, but just right before he was to depart Tokyo-03, Misato understood the real nature of Shinji's personality and went to get him back before he departs, Shinji still hesitant from leaving Tokyo-03 did not board the train and Misato took him back to active duty.

episode 5
Rei I

In the beginning of the episode we see a failed synchronization test of another pilot named Rei of another Eva called Eva-00. In this mishap, Gendou got his hand injured after trying to save Rei and opened an overheated entry-plug port door. In this incident, Gendou's glasses cracked and it is this glasses that Shinji discovered in Rei's room when he visited her in her place. Rei treasures Gendou's glasses very much. Near the end of the episode the 5th Angel attacked and Shinji's Eva-01 was heavily damaged after being hit by an intense particle beam.

episode 6
Rei II

After Shinji recovered from his injuries after being struck by a particle beam from the 5th Angel, both Shinji and Rei was despatched to defeat the Angel by using a proto type positron rifle. Apparently this Angel strikes down any moving body in a definite distance around it and the only way to defeat it was to use a positron rifle with Rei and her Eva-00 protecting Shinji as his Eva-01 fire at the target. The first shoot missed but the second shoot destroyed the angel just the moment the Angel's drill penetrated Geofront.

episode 7
A Human Work

Not all of the enemies are angels, in this episode, a government project known as JA tried to produce a robot to substitute the Eva robots of Nerv and Gendou feeling that this could hamper the main objective of Nerv sabotaged the project and on the day of the debut of the JA robot, it malfunctioned, and with the danger of over heating and nuclear blow-out, Misato tried to stop it by getting inside the JA robot with the help from Eva-01 and stopped it in time, not because of Misato's efforts but it was a sabotage plan that will terminate just before the self destruction of the robot.

episode 8
Asuka Strikes!

In this episode, the 3rd Eva robot Eva-02 was introduced and so was its pilot, Asuka Langley. The UN fleet was on its way to deliver the robot when the 6th Angel attacked. The angel attacked because it was looking for what Kaji, a special Nerv agent, was bringing to Japan. Shinji, Misato, Kensuke and Touji was there when the angel struck and with the high spirits of Asuka, she and Shinji entered Eva-02 and went to fight the Angel, it was the first fight under water and the Angel was defeated by a plan of Misato of sinking 2 ships and firing inside the Angel with the help from Eva-02.

episode 9
Both Of You, Dance Like You Want To Win

Asuka already graduated University in Germany but still entered the same class of Shinji along with Rei in their junior highschool. Asuka was instantly the most popular girl in school but because of her egotistic attitude this slowly changed. It was this time that the 7th Angel attacked and after Asuka's Eva-02 tried to cut it in half, it produced another twin of itself and soon after both Eva-00 and Eva-01 was thrown far away. Apparently the Angel can only be defeated if both sustained the same damage at the same time and it was this fact that Misato decided that both Shinji and Asuka stay under her direct supervision and synchronize their battle moves, after 3 days they did and they defeated the Angel.

episode 10
Magmadiver

An angel was discovered still in its pupa phase inside a volcano when Nerv decided to capture it alive and sent Eva-02 to retrieve it but after it was captured, it grew and became the 8th Angel and the fight between Eva-02 and the Angel was won by Eva-02 when Asuka decided to freeze the core of the angel and pierce it but just after the angel went down it cut the lifeline that connects Eva-02 and just when the it was cut, Eva-01went inside the volcano to save a sinking Eva-02.

episode 11
The Day Tokyo-3 Stood Still

When the 9th angel attacked, all of Geofront and Tokyo-3 was without power, but despite this fallback, Rei, Asuka and Shinji was able to enter Nerv and proceed to the hangar of the Eva robots, where they were met by Gendou, Dr Akagi and company who were preparing the launch with manual procedures. With less then 5 minutes of internal power, the 3 decided to work out the plan of Asuka and defeated the angel who was trying to penetrate Geofront by spilling some acidic liquid inside. It was the first time the 3 worked as a team.

episode 12
She Said "Don't make others suffer for your personal hatred"

Misato was promoted to 3rd Class Colonel and 3rd in command of Nerv. It was this time the 10th angel attacked coming down from orbit. In this episode we discovered that the main reason that Misato joined Nerv was to revenge the death of his father who was killed in the Katsuragi Expedition back during Sept 13, 2000 when the 2nd impact occured. The 10th Angel was on a direct course toward Tokyo-3 , and with Gendou and Fuyutsuki (2nd in command) absent, she risked a plan and ordered the 3 Evas to intercept it just before touchdown which they did despite amazing odds and with the effort of Shinji, defeated the Angel.

episode 13
Lilliputian Hitcher

The 11th angel attacked Nerv by hacking and cracking the Magi system. These angels are colonies of microscopic entities that can penetrate a computer. The Nerv's super computer is known as Magi which is divided into three parts: Melchor-1, Balthasar-2 and Casper-3, and it is set to self destruct the moment all three was completely compromised and with out the Eva robots, Dr Akagi, was racing with time to retrograde the angels who was cracking out the computer like a virus and with less than a second to spare, the treat was halted.

episode 14
Weaving a Story

A flashback from the other episodes and the discussion between Gendou and the Human Complement Committee on the schedule of Seele's plan to implement the Human Complement Program right after all the angels are defeated. This episode also puts some insight to the nature of Rei - " A women who sheds no blood" (no menstruation).

episode 15
Those Women Longed For The Touch Of Other's Lips And Thus Invited Their
 Kisses

Misato feeling the years creeping up on her falls in love with Kaji again, her boyfriend back when they were still in the university. It is also this episode that we see for the first time Shinji and his father together to visit the empty grave of his mother who died in the year 2004. On another note Kaji was investigating the deep dark secrets of Nerv in Kyoto and also we see for the first time the kissing of Asuka and Shinji. In the last segment of the episode we saw a giant nailed to a red cross with a spear pierced in its chest.

episode 16
Splitting Of The Breast

Finally Shinji topped the synchronization test among his comrades Asuka and Rei, and this gave Shinji a boast in his confidence. It was this feeling of over confidence that got him to be careless when the 12th angel attacked. He was sucked in along with his Eva-01 to another dimension inside the angel and it was here that we saw the spirit that resides inside Eva-01: Shinji's mother. After over 12 hrs inside and just before Shinji's death due to lack of energy to power the life support system. The Eva-01 unexpectedly revived and forced itself outside, killing the angel in the process and revealing that Eva-01 is different from the other Eva robots, that even without power, it can move in drastic times. It was because of this that Shinji's life was saved.

episode 17
Fourth Children

Eva-04 which was being built in Nevada USA was lost when it disappeared along with the branch of the Nerv facility there and it was decided that the now finished Eva-03 was to be sent to Japan so not to duplicate the incident that happened in Nevada. With the Eva-03 coming to Japan, another pilot was be selected and the person who bullied Shinji before was chosen to ride it. With mix feelings, Touji accepted under the condition that his injured younger sister be transferred to a better medical facility.

episode 18
Ambivalence

The Eva-03 arrived 2 hrs late after passing thru a strange cumulus cloud. It was during the synchronization test that it was revealed that the Eva-03 was infected by the 13th angel and went amok and destroyed the facility in a big explosion. The Eva robots was called to intercept but Eva-00 and Eva-02 quickly fell and only Shinji was left, he hesitated to fight because he fears that he might harm whoever is piloting the infected Eva but Gendou wouldn't have of it and he ordered the dummy plug to be activated and override the system to eliminate the threat and the Eva-01 responded and ripped Eva-03 to bits and crashed the entry plug before Eva-01 stopped. Shinji wasnt able to do anything.  Misato, Asuka and Rei knows who the 4th children (pilot) is  but Shinji doesnt and Touji wouldn't tell, so when the salvage team arrived to eject the pilot from the broken entry plug, he was suprised to see it was Touji.

episode 19
Introjection

Shinji was boiling mad and wouldn't eject out of the entry plug, he wanted to destroy Nerv for what his father did to Touji, but despite his cutting all command connections of Eva-01 to the Nerv Central Command,  they were able to stop him by raising the LCL pressure of his entry plug to
dangerous levels. During his hospitalization, we see both Shinji and Touji
on the same room, Touji lost his right arm and right leg. When Shinji recovered he resigned from Nerv and just when he was about to leave Tokyo-3, the 14th angel attacked, it was so powerful that it penetrated  Geofront and even with Asuka's resistance, Eva-02 sustained heavy damage.  The angel even penetrated the central command and it was this time that Shinji, seeing the damaged Eva-02 and hearing the advice of Kaji, went back to Nerv in his own will and with the permission of his father boarded Eva-01. Eva-01 almost defeated the angel when it ran out of power and we see the angel piercing the frozen Eva-01 and ponding the core of the Eva when Shinji's synchronization exceeded 400 % and that made the Eva move again. The Eva-01 was again out of control and in the end eated the angel.

episode 20
Weaving A Story 2: Oral Stage

Shinji was lost inside Eva-01 (disappeared) when he hit 400% synchronization and despite the salvage efforts of Nerv it took them almost 31 days before Shinji decided to return. During this time Shinji was battling whether to stay inside and be one with the Eva or go back. Misato cried when he saw Shinji materialized.

episode 21
He Was Aware That He Was Still A Child

In this episode we saw the birth of Nerv. Misato was the only person to survive the 2nd Impact when his father put him in an escape pod before the expedition was wipe out. For 2 years Misato was catatonic and was unable to speak. Prof Fuyutsuki was investigating the real cause of the 2nd impact when he bumbed into unexplained pictures and the mysterious orgnization called Seele. He went to Gendou to demand an explanation when Gendou showed him the real purpose of Seele and asked his help to fight and deceive them, which he agreed. Geofront was still being constructed and also the Magi computer. Here the first clone of Rei was introduced which was later killed by the inventer of the Magi Computer Dr. Naoko Akagi (mother of Dr. Ritsuko Akagi)  and her subsequent suicide. Yui, the mother of Shinji was also introduced and it was shown that she disappeared inside an Eva robot during a synchronization test. Back in the year 2015, Kaji kidnapped Fuyutsuki but later returned him after being interrogated by Seele members. The next scene we heard Kaji being shot.

episode 22
Don't Be

In the first scene we see the nigthmares of Asuka were she saw her mother commit suicide after her mother was psychologically poisoned after a failed synchronization experiment with an Eva. The neglect of her father and her wish to grow up without the help of others has forced her personality to be arrogant and egotistic. At this point she has entered the menstruction period and that has also affected her synchronization with Eva-02. As her body under goes several changes, she starts to exhibit erratic behavior and start to spark out at Shinji and Rei. It was this time that the 15th angel appeared above earth orbit, unmoving, but Nerv decided to attack, Rei was sent to use a positronic rifle to knock it off orbit when Asuka decided to do that on  her own. When Eva-02 was about to fire, the angel attack Asuka telephatically, poisoning her psychologically and raping her thoughts. Rei fired her  positron rifle but it was deflected by the AT field so what Gendou decided was to use the Longinus Spear that was pierced at the large entity beneath  Nerv and throw it into orbit killing the angel. Asuka suffered psychologically and wasn't able to pilot an Eva again in the TV series until the Movie:Rebirth.
 

episodes 23/24
Rei III / The Beginning And The End, or "Knockin' on Heaven's Door"

Seele was furious about losing the spear and with Gendou using it without permission and they were discussing it with Gendou when the 16th Angel appeared. The 16th angel was hovering above Tokyo-3  when Rei was sent to intercept. When the angel noticed her presence, it attacked her and infected her, Shinji was sent to help Rei when Rei sense that Shinji will be infected too unless she does something and that something was to self destruct her Eva-00, with a part of the Angel lock in her Eva, the angel was destroyed when it exploded and taking the whole Tokyo-3 with her as well, water gushed inside Geofront.
The next scene we see a Rei (3rd clone of Rei) meeting a suprised Shinji and later we see that Rei untie her bandage to reveal no injuries whatsoever. Seele sensed the treachery of Gendou and to stir-up trouble at Nerv they punished Ritsuko and send her back to Nerv. Ritsuko feeling betrayed by Gendou called Shinji to come to Nerv and the next scene we see Misato pointing a gun at Ritsuko, asking her to reveal everything that she knows. Ritsuko showed Shinji and Misato the true nature of the Eva and also the true nature of Rei. Later Ritsuko killed all the clones in front of the eyes of Shinji and Misato and was later court-martialed by Gendou.

Shinji now knows that Rei was part-clone of her mother and avoided her, and with Tokyo-3 gone all his classmates transferred somewhere else. Seele sent the pilot to replace Asuka, the fifth children known as Kaoru. Kaoru quickly became Shinji's best friend. Later when Kaoru thought it was time, he revealed himself as the 17th angel over a surprised and angry Shinji. Kaoru took Eva-02 to the terminal dogma and Eva-01 intercepted. Eva-02 and Eva-01 fought with Shinji winning and Kaoru went to find Adam, the 1st Angel when he discovered that the giant creature in the cross is not Adam but Lilith and with another thought he let Shinji grab him and asked Shinji to kill him, or else the world will suffer if he lives. The 3rd clone of Rei was watching above, and Kaoru told Rei how they are similar (Rei produced an AT field here). Shinji decided to kill Kaoru to save mankind but he didnt forgive himself for what he did.

episodes 25/26
Do You Love Me? / Take Care Of Yourself

Shinji withdrew from the world and the next scene we see him battling his
conscience. Why did he kill Kaoru? Why does he ride Eva-01? Here we see glimpse of reality. Asuka inside the entry plug beneath the lake, Misato beside a wall tainted with blood, unmoving. A dead Ritsuko floating on LCL. And at the end of the episode the Human Complement Program was initiated.

The human complement program has begun and we see Shinji trying to deal with it in his conscience. And then we saw a glimpse of an alternate reality. In it we see Rei, so energetic and full of life like an ordinary kid. The way she got angry at Shinji for looking at her panty (accidentally). The way Shinji acted like a normal 14 year old, receiving a slap from Asuka who went to wake up Shinji and saw his erected thing under his shorts, Asuka shouted " HENTAI!!!" and Shinji shouted back,"What do you expect! Its morning!". Then we see Yui and Gendo like a Typical Jap Family. In that scene, Rei was not related to the Ikari Family, Gendou was never the head of Nerv, Yui is still under the research lab of prof Fuyutsuki (and so his Gendou). Shinji was a normal, smiling kid. Touji still has his left leg and left arm. Kensuke, all depressed that finally the war with the angels is over,"Peace finally" he said and everybody was going back to Tokyo-03. Misato was Shinji's class home room advisor (still with that cool car- with a teacher's salary its difficult to believe). We see Shinji, Touji and Kensuke showing the "V" sign to a cool walking Misato. Shinji seeing this realized that reality is in the eyes of the beholder and we see a smiling Shinji after he was humanly complemented.