3 years ago, when she started all the chaos, she met someone who looks like Kyon. A Mr John Smith. That's why she chooses Kyon as the first member of the SOS-dan

3 years ago, there was an incident which leads to:
- Some ppl gaining physics power (like itsuki)
- Ppl from the future cannot go back beyond the year of the incident
- Alien detect a data explosion from earth, and the cause was haruhi

Thus ppl with physics power believe that haruhi had altered the timeline somehow, making all people in that time going into another world which she created and can manipulate, like a world inside Haruhi's dream. This and also the ability of Haruhi to subconciously control the world makes the ppl of the Organization regards her of the god of this alternate world. Itsuki is given the task of keeping an eye for her so that no harm can get near.

The alien, who was monitoring Integrated Data Sentient Entity, sends two humanoid, Nagato Yuki and the class rep (as her backup) to monitor Haruhi.

The future ppl meanwhile send mikuru to find out what really happen and why does the timeline seems to have glitched 3 years ago.

Due present day, 15 year old Haruhi craeted the SOS-dan and recruited Kyon, as he looks like the person she met 3 years ago, a Mr John Smith

Kyon, even tho he's normal, seems to nullify her control of the world, such as she(Haruhi) lost the draw strawing lot to determine who will partner Kyon much to her anger and jelousy (Ep 5)........
Itsuki thus recognise him as an important person to Haruhi and the only person that can control her (she meekly forfeit the baseball tourney because Kyon asked so).

it will appear when Haruhi is in a bad mood

Order aired - Episode title/description [Chronological order]
01 - Asahina Mikuru no Bouken 「朝比奈ミクルの冒険」 [00]

Bunkasai movie made by SOS-dan.
Came from: second novel “Suzumiya Haruhi no Tameiki”.
02 - Suzumiya Haruhi no Yuuutsu I 「涼宮ハルヒの憂鬱I」 [01]

Introduction of Haruhi.
Formation of SOS-dan.
03 - Suzumiya Haruhi no Yuuutsu II 「涼宮ハルヒの憂鬱II」 [02]

Yuki’s secret.
04 - Suzumiya Haruhi no Taikutsu 「涼宮ハルヒの退屈」 [07]

Baseball game.
Came from: first half of the third novel “Suzumiya Haruhi no Taikutsu”.
05 - Suzumiya Haruhi no Yuuutsu III 「涼宮ハルヒの憂鬱III」 [03]

Yuki’s secret further explained.
Itsuki joins the club.
Mikuru’s secret.
Itsuki’s secret.
Kyon makes Haruhi angry.
06 - Kotou Shoukougun (zenpen) 「 孤島症候群(前編)」 [09]

It’s summer! SOS-dan goes to the beach.
Came from: third novel “Suzumiya Haruhi no Taikutsu”, the same book as the baseball game.
07 - Kotou Shoukougun (kouhen) 「 孤島症候群(後編)」 [10]

Continues from above.
More swimsuits and wet Mikuru scenes.
08 - Suzumiya Haruhi no Yuuutsu IV 「涼宮ハルヒの憂鬱IV」 [04]

Ryoko tries to kill Kyon.
Yuki stops her with l33t SQL queries.
Ryoko disappears.
09 - Filler Episode Based on Third Novel [08]

Since this episode is chronologically supposed to be between the episode 4 (chapter 1 of novel 3) and episode 6-7 (last two chapters of novel 3), then it makes sense for it to also be about an event from middle of the third novel, “Suzumiya Haruhi no Taikutsu”.
10 - Suzumiya Haruhi no Shoushitsu I 「涼宮ハルヒの消失I」 [11]

Ryoko returns in this episode.
Came from: fourth novel, “Suzumiya Haruhi no Shoushitsu”
11 - Suzumiya Haruhi no Shoushitsu II 「涼宮ハルヒの消失II」 [12]

Continued from above.
12 - Suzumiya Haruhi no Yuuutsu V 「涼宮ハルヒの憂鬱V」 [05]

Kyon is brought into the Sealed Dimension by Itsuki and faces a Giant of Light for the first time.
He unknowingly makes Haruhi unhappy again.
Came from: end of the first novel, “Suzumiya Haruhi no Yuuutsu”.
13 - Suzumiya Haruhi no Yuuutsu VI 「涼宮ハルヒの憂鬱VI」 [06]

The end of the world. Almost.
Kyon kisses Haruhi and stops the world from being destroyed.
Life continues on as per “normal”.
This is the end of the first novel.
14 - Suzumiya Haruhi no Tameiki 「涼宮ハルヒの溜息」 [6.5]

This is the start of the second novel.
Chronologically speaking it should be between Yuuutsu VI [06] and Taikutsu [07].
Haruhi suddenly decides for SOS-dan to take part in the bunkasai (cultural festival) by making a movie… and you know how it goes from here.