Raiden Fighters Jet has non-linear stage progression. How well you play affects what Stage you will be sent to after you complete it. You cannot play through every stage in Raiden Fighters Jet in a single session. At the end of each simulation level, you are graded on three criteria:

• Ability: This is a cumulative bonus calculated by destroying enemies, chaining bonuses you find, and collecting medals.
• Medals Earned: This keeps track of how many medals you collect in each individual stage. Medals that you blow up to enter the 100,000-point Golden Medal mode do not count towards this bonus. Also, medals you lump together to form a "mega-medal" will count as the number of regular 100pt medals you used to lump that particular "mega-medal" when you collect it.
• Technical Points: This criterion makes up a major part of your bonus tally. It effectively determines what stage you will play next. The most Technical Points you can collect in any simulation level is 10 (Level 30 max for Technical Points is 8; there are no Fairies and Micluses in Level 30). The number of Technical Points will act as a multiplier to determine your final bonus score at the end of each simulation level. It is possible to get up to 12 million points in bonus points! The breakdown of the Technical Points criterion:
  • Not dying in the level: +5
  • Enemy destruction: up to +3 (I believe this criterion has something to do with how many medium-sized enemies you destroy. On some levels, Quick Shotting certain large enemies will get more of those same large enemies to appear)
  • Finding at least oneMiclus in the level: +1 (To get a Technical Point, you have to shoot the Miclus to make him disperse 9 medals, then explode for 100,000 points. You don't have to find every single Miclus hidden in a particular level. To get this Technical Point, just make sure you blow up (haha) every Miclus you uncover. Cannot run Technical Point total for a particular level past 10.)
  • Collecting at least one Fairy in the level: +1 (Killing a fairy or letting it leave the screen will deduct one Technical Point. You don't have to find every single Fairy hidden in a particular level. To get this Technical Point, just make sure you collect every Fairy you find (to be exact, 80% of fairies discovered should be collected). Cannot run Technical Point total for a particular level past 10. Note: Expert players can employ fairy killing to prolong their chains. Whether or not this is a good idea depends on whether it would bring you down the 80% collected-to-discovered ratio versus how many points you would get in the chain.)

Beginning on LEVEL 05, your path of progression will be determined by how well you play. The stage you enter next depends on how often you die and your play technique, which is graded at the end of each simulation level.
 
 

Stage Progression Chart

You actually have some control over the slave formation you want. The formation depends on the number of lives you have plus the number of bombs you have. Slaves only assume these formations if you collect a Slave icon when you already have 2 slaves. Additionally, the slaves automatically assume these formations when you play as the secret fighters. Playing as the any of the seven standard planes, the Hell Diver, and the Ixion, requires you to use a charged attack in order for your slaves to assume these formations. You can only change the formation if you collect a bomb or lose a life (!) as the seven standard planes, the Hell Diver, and the Ixion. As the secret fighters, you need to collect another Slave icon after your "Formation Sum" changes. This secret is also present in Raiden Fighters 1 and Raiden Fighters 2.
 
 

Raiden Fighters Jet allows you to select from up to three different game modes. These game modes are enabled via software settings in the machine. When these game modes are enabled, an interstitial screen pops up prompting you to select a game mode before you select your fighter. These game modes are also available in Raiden Fighters 2.
 

To play as the secret fighters (Raiden mk-II, Judge Spear and their blue counterparts; Miclus), do the following:

• Insert coin, and then press the Start button and these buttons simultaneously: P1 Fire, P1 Bomb, P2 Fire, and P2 Bomb. This means you should press five buttons simultaneously. You should see the secret fighters on the Fighter Selection Screen.
• To play as the slaves of any of the fighters, highlight any fighter and then press P1 Fire, P1 Bomb, P2 Fire, and P2 Bomb simultaneously again. You should be able to get the Slave plane of the fighter you selected. Selecting the Miclus will allow you to play as the Fairy. Slaves inherit the speed and the bombs used by the fighters they normally accompany.

Miclus: You can see the tail of a gigantic bomber on the right side of the screen after the boss starts moving. Stay above the center of the tail for a while.(100,000 points)
Fairy x 3: Just before seeing the boss there are a maximum of three big tanks (get the third tank by Quick Shotting all eight medium planes). Destroy the turret on each of them and leave the bodies alone. A fairy will appear from each tank.(100,000 points)

• To get a 3rd train in LEVEL 05: There are two ways to do this. The first method is to build up a "mega-medal" and don't collect it.Have your Slaves tow the "mega-medal" into the next stage, LEVEL 05.The third train will appear near the beginning of LEVEL 05.The second method is to already have the RF1/RF2 Golden Medals appearing.This secret is courtesy of Wolfgang Zellermayer.

DX Bonus x 3: There are a maximum of three trains that appear moving horizontally across the screen. Don't shoot the trains until all of the train is fully onscreen. You need to destroy every part of the trains (engines and all boxcars) to collect the DX bonuses (100,000 points each).
Miclus x 3: Placed throughout the level are three large round turrets.Do not destroy these turrets. Instead, hover above each as you encounter them. The turrets will explode, and a Miclus will appear from each. (100,000 points each)
Fairies: At the middle of the level, you'll see a crane with a moving arm. Don't destroy it! Overlap the crane and "paint" the entire crane with your ship by moving left and right along the crane. If you are successful, the crane will explode, giving you many fairies, plus a Multiplier if you're able to chain this bonus with others you've collected a few seconds earlier. (100,000 points each, base Multipler = x2)

• Miclus: When the screen begins to start scrolling left, you'll see a pile of crates near the beach. Don't destroy it! Let the tank above the crates collide with it and a Miclus will appear. (100,000 points)
• Stage progression notice: If you don't die in this level, you'll be taken to LEVEL 20. Otherwise, your game will end here.

• Fairy: Quick Shot all of the medium planes in the beginning of the stage. (100,000 points) 
• Fairy x 2: If you let the boss live long enough, do not destroy the final tank that appears on the top right portion of the screen. Let it alone and it will soon self-destruct, releasing two fairies. Collect these two Fairies quickly, while the "DISCOVERED FAIRIES" message is still on the screen, and you'll get a Multiplier of x2! (100,000 points x2) 
• Fairy x 2: When the Tank Boss appears, you will see two small tanks appearing from the left and right sides. Don't destroy these tanks. The Tank Boss will ruthlessly crush these two tanks, and each will release a Fairy!
• Miclus: Before the river, you'll see a small clearing in the jungle on the right side.Hover over to the upper-right of the clearing and a Miclus will appear.(100,000 points)
• Miclus x 2: There are two small bushes located on both sides of a medium sized tank. Hover over each bush to uncover a Miclus. (100,000 points each)
• Stage progression notice: Play exceptionally well and lose no lives, and you'll be taken to LEVEL 30. Otherwise, you'll be taken to LEVEL 20.

 

Fairy x 2: Before the boss, you'll see two big tanks. Destroy their turrets and leave the bodies alone. A Fairy will appear from each tank. (100,000 points each).

• No secrets in this level. You can rack up a ton of x9 Quick Shots in this level if you are powerful enough.
• Stage progression notice: If you have lost one life overall, you'll be taken to LEVEL 40. If you haven't died at all, you'll be taken to LEVEL 45.

• Fairy: Quick Shot the midboss of this level, which is a red version of "Hummingbird," the menacing black plane boss from Raiden Fighters 2..A Fairy will appear if you are successful.
• Stage progression notice: If you have been playing poorly up to this stage, this will be the last stage for you and the game ends here.Otherwise, you may be taken to LEVEL 40 if you've lost just one life in your current game, or LEVEL 45 if you haven't died yet.

• No secrets in this level.
• Stage progression notice: After you complete this level, to get to the real battle levels, PHASE 1 and PHASE 2, you will need to have satisfied ALL of the following requirements:
• Don't die in this level.
• Quick Shot every medium plane in this level.You need to Quick Shot the first medium plane that appears to get the second one to appear, and so on, until you have made four more of these planes appear.Miss a Quick Shot, and no more medium planes will appear, nullifying this requirement.You should see five Bomb icons floating around on the screen if you completed this requirement.
• You must have the RF1/RF2 Golden Medals appearing.
If you don't meet any of these requirements, you'll be taken back to LEVEL 35 if you have lost two lives in your current game. If you've lost one life, you'll be taken to LEVEL 50. However, obtaining a VERY GOOD technique bonus in this level can promote you to real battle PHASE 1, but don't count on it.

Miclus: Quick Shot all of the medium-sized planes that appear at the beginning. The planes appear from the top of the screen in this order: Left, Right, Center, Right-Center, (delay ~2 seconds), Left. A Miclus will appear from the red circle in the picture, above the medium-sized ice floe on the left. Miclus: Hover over the area circled in yellow for a few seconds. A Miclus will appear. MEGA Bonus Chain: Quick Shot the first 3 medium planes (20,000 - 20,000x3) Quickly move up to the area circled in yellow to uncover Miclus #1. DON'T shoot the Miclus yet! (Multiplier x4) Quick Shot the last two medium planes (20,000x5 - 20,000x6) Miclus #2 will appear from area circled in red. DON'T shoot this Miclus either yet! (Multipler x7) Immediately Bomb the Submarine that surfaces on the right side of the screen. The Bomb will wipe out the three small ammo batteries before destroying the bigger one. Grab the Fairy without waiting for it to release a Bomb (100,000x9) Shoot both Micluses that are on the medium ice floe on the left. Both will be worth 100,000x9 points each!! If you are quick enough, you can Quick Shot the medium-sized tank sitting on the ice floe on the right side, after the first Submarine. (50,000x9) Grand points total: 3,490,000 pts!

Miclus: On the right side of the huge submarine boss, you'll see a tiny ice floe. Hover over the area (in the water) just above the tiny ice floe for a few seconds. A Miclus will appear. (100,000 points)

• Fairy x 2: Simply destroy the two big tanks in this level.
• Fairy: After destroying the second big tank, you'll see three medium tanks. Destroy the turrets on each of them and leave the bodies alone. A Fairy will appear.
• Stage progression notice: After completing this level, your game will end here, and you'll be presented with the second ending (the first ending appears if your game ends at LEVEL 35).

• No Secrets in this stage, but you can expect swarms of medium and large planes coming at you here! Insane level.
• Stage progression notice: You will move on to PHASE 2 no matter what. Notice that you are not scored on techniques at the end of this level. Try not dying in this level...

• Miclus: At the very beginning of the stage, hover over the bottom-right corner of the large building on the left side of the screen. A Miclus will appear.
• Miclus: On the left side, you'll see a building similar to the first one where you found the first Miclus, with two grounded planes located across to the right. Again hover over the bottom-right corner. A Miclus will appear.
• Fairies: Thoughout the level, you'll see 12 medium tanks. Destroy the turrets on each tank you encounter and leave the bodies alone. A Fairy will appear from each tank. 
• Miclus: After the first four medium tanks, which are placed in a 2 rank, 2 file arrangement, you'll see another building on the left side. Once again, hover over the bottom-right corner. A Miclus will appear.
• Fairy: Instead of ending the game, the Phase 2 Tank Boss will release a Fairy after you destroy it when you've completed the prerequisite to fight the True Final Boss (see below.)
• To fight the True Final Boss in the NORMAL mode: To reach the True Final Boss, don't die in Phase 1 at all! The True Final Boss is a huge bomber plane that looks very similar to "Hummingbird" from Raiden Fighters 2. You need not worry about how many lives you lost in Phase 2. However, you will not fight the True Final Boss if you continue your game. When you defeat the Phase 2 tank boss in the NORMAL game mode, it will release a Fairy (instead of ending the game). Afterwards, you'll get to fight the True Final Boss! In the SPECIAL game mode, you will encounter the true final boss no matter what.
• Stage Progression Notice: After completing this stage, your game will end here. If you complete the game by destroying the Tank Boss, you'll receive a 1 million point endgame bonus. If you defeat the True Final Boss, you'll receive a whopping 10 million point endgame bonus, and you'll get to see the best ending.

Raiden Fighters Jet has various hidden bonuses. You can earn many bonus points if you can uncover these secrets. When you uncover a secret, a message appears on the top center of the screen. Most of these bonuses are present in the first Raiden Fighters and Raiden Fighters 2.
 

QUICK SHOT! (10,000 pts - 100,000 points)

Killing a large enemy before it has a chance to fire at you. In Raiden Fighters Jet, the more Quick Shot bonuses you collect, the more enemies that hold bonuses (Slave Icons, Bombs, and Fairies) appear!

DESTROYED AT A TIME! (100,000 points)

Destroying two special targets within one second of each other.

DISCOVERED THE FAIRY! (100,000 points + Bomb)

The Fairy is a hidden character in the original Raiden series. She gives you one Bomb (wait for her to release the Bomb icon first) and 100,000 points if you collect her.

KILLED THE FAIRY! (10 points)

Your weapons can hurt the Fairy. Be careful where you drop bombs too.

DISCOVERED THE MICLUS! (100,000 points + 9 medals)

This little blue critter is Seibu's mascot. In the Raiden Fighters series, he spits out 9 medals when you shoot him, then he explodes. To make him appear, you hover over certain places or perform certain tasks. The Miclus is helpful in building up to the 100,000 point medals.

DX BONUS (1st: 100K, 2nd: 200K, 3rd: 400K points)

In LEVEL 05 only. You get this secret if you destroy every part of one of three trains that appear. You have to wait for all of the train to appear before you destroy it. Incidentally, this is the very same secret that is in the final phase of Raiden DX's Mission Alpha Stage.

BONUS EVENT CHAINING (bonus value x Multiplier)

If you can collect  bonuses (Miclus, Fairy, Quick Shot) one after the other quickly, their point values will be multiplied. The duration that bonus chaining can be performed is indicated by the presence of any Secrets Messages on the top-center of the screen (i.e.DISCOVERED THE MICLUS). Each additional Chained Bonus will increase the Multiplier by one to a maximum of 9. This means the maximum point value of a Chained Bonus is 900,000 points (Fairy/Miclus and a Multiplier of 9)! When every Event Message disappears off the screen, the Multiplier is reset to 1.

Descriptions of Bonuses translated from Abfuku's Raiden Fighters Page (雷電フリークス)

Very many thanks to Wolfgang Zellermeyer,Calvin Thoong Boon Yap Kevin Dart, and Lynx for all of these secrets! Also, thanks again to Wolfgang Zellermeyer for valuable stage progression information.

Screenshots from replays by CYM, LIM, Alamone, and tiw.