The most relevant chapters for the Star Wars plot

Several

1x01  Ambush

1x13  Clash of Jedi

1x14 - Defenders of Peace

1x15  Transfer

Mace Windu and Boba Feet

2x20 - Death Trap

2x22 - Death Tracking

2x21 - R2 Heading Home

Grievous and Kenovi

1x10 - Grevious's Lair

2x09 Grievous Intrigue

The God of the Star Wars universe

3x15 Gentlemen

3x16 Kidnapped

3x17 Ghosts of Mortis

Sisters of the night

3x12 Sisters of the Night

3x13 Monster

3x14.The.Witches.of.the.Bruma.

4x19 Massacre

Clone psychology

1x01 Ambush

2x10 - The Deserter

4x06.Droids.Nomads (This chapter shows the indifference towards droids by the clones)

4x07.Shadows.in.Umbara.

4x08.The.general

4x09 A Discrepancy Plan

4x10.La.masacre.Krell.

Ashoka tano

(Ashoka Tano makes her first appearance in The Clone Wars movie)

5x17 Sabotage.

5x18 The Jedi Who Knew Too Much

5x20.The.Jedi.Wrong.

5x19 Catch a Jedi

Darth maul

3x13 Monster

4x22 Revenge

4x21 Brothers

5x13.point.no.return.

5x14 Eminence

5x15 Shadows of Reason

5x16 The Lawless.

The case of Fives and Order 66

6x1 The Unknown

6x2 Conspiracy

6x3 Fugitive

6x4 Orders

The Saifodias and Yoda Affair

6x10 The Lost

6x11 Voices

6x12 Destiny

6x13 Sacrifice