The definition of the All Stages category is to complete the game along with all 8 maverick stages. This category primarily uses Zero for every stage up until the 8 maverick stages and the first two virus stages are completed, then X is used to obtain the ultimate armor to finish the game with it, as Zero can no longer SDC reliably after obtaining Skiver's weapon.

Routes

Notes:

• The parenthesis next to each boss name refers to whether you should get life or energy at the end of the maverick fight. If there is none, then it is up to the player's choice as the resulting part doesn't matter. Get life if you want to take more hits, or energy if you want more dark hold and/or giga attack.
• Mattrex's stage is generally done early, as his parts are near useless, and his weapon is useful for Grizzly Slash's stage.
• Note that you fight Dynamo after two mavericks, and again after six mavericks.
• Skiver is always fought last, as defeating him disables Zero's ability to SDC any more. However, you can save a little time by launching the shuttle early (if the enigma shot failed) before Skiver, then doing Virus Stages 1 and 2 to be able to SDC both bosses (especially the eyes in Virus 2), and then fighting Skiver before obtaining the Ultimate Armor. You should ALWAYS follow this route if the enigma shot succeeds, as there is no reason not to. Assuming the enigma shot fails, however, doing Skiver after the first two virus stages is riskier as the shuttle has a higher chance of failing.
• After Virus 1, 2, and Skiver, regardless of which order you do them in, the endgame route is always to use X (unarmored) on Virus 3 to get the Ultimate Armor, then use Ultimate Armor X in Virus 4.
• All routes below are for single-segment purposes. In other words, it is assumed that enigma/shuttle first are NOT done.

GA-Rank Route

1. Mattrex
2. Grizzly Slash (Energy)
3. Duff McWhalen (Energy)
4. Axle the Red (Energy)
5. Dark Dizzy
6. Izzy Glow
7. Squid Adler (Life)

This route is the fastest known route, but also the most difficult, as it requires you to have Zero at GA rank after Mattrex's Stage. This means to complete the stage quickly, take less than 16 damage, and kill as few enemies as possible. The reason is that you can immediately do Grizzly Slash second, as Grizzly should be at level 9 instead of 7, thanks to being at GA rank. In addition to that, you fight Dynamo after Grizzly, and hyper dash is not as useful for Duff's stage, so you get hyper dash before Axle's stage, as opposed to three stages later in Sneaky's route.

Duff's stage is done third as a buffer to wait a stage for hyper dash; Zero's ability from Duff is also useful for Axle's stage.

Axle's stage is done fourth, and after Duff, since Duff's ability is useful for this stage, and Axle's stage here nets you Z-Saber Plus just before Dynamo 2.

Dark Dizzy is done before Izzy since Dark Hold is most useful in Izzy Glow's stage. Izzy Glow is done before Squid Adler, as the giga attack is useful for Squid Adler's stage.

Dark Hold Route

1. Dark Dizzy
2. Mattrex
3. Grizzly Slash (Energy)
4. Axle the Red (Energy)
5. Duff McWhalen (Energy)
6. Izzy Glow
7. Squid Adler (Life)

This route focuses on getting Dark Hold as early as possible, but at the cost of not having hyper dash for Dark Dizzy's stage. While this is slower than GA rank, Dark Hold makes several obstacles easier in later levels (particularly Mattrex, Axle, and Izzy Glow's stages).

Grizzly Slash is done third as usual to get hyper dash before stage 6. Axle 4th to get Z-Saber Plus (and so you can use it to fight Dynamo 2), Duff is 5th to get W-Energy Saver. Izzy is done before Squid since giga attack is useful on Squid Adler's stage.

Credit to luiz_miguel for this route.

Sneaky Route

1. Mattrex
2. Duff McWhalen
3. Grizzly Slash (Energy)
4. Axle the Red (Energy)
5. Dark Dizzy
6. Izzy Glow
7. Squid Adler (Life)

This route is the route to fall back on if you did not get GA rank in Mattrex. Mattrex is done first as his ability is useful for later stages; Duff is done second as it is the stage where the lack of hyper dash loses the least amount of time. The rest of the route is standard, getting hyper dash then z-saber plus as early as possible. The disadvantage to this route is that because Duff is defeated second, Duff will not be at least level 8, so the player will lose out on W Energy Saver.

Credit to sneakytkdninja for the basis of this route.