I'm at the Mutant Protopet battle on Going Commando in the R&C HD collection. I thought the battle was too hard for me, so I decided to go to the first game, which I already completed. I grinded through the first game to get the R.Y.N.O. After I got the R.Y.N.O., I got back to Going Commando to see if it was free, but it wasn't. I thought beating the first game with the R.Y.N.O. would make the 2nd one free but it still isn't. So if you could tell what I'm doing wrong I really appreciate your answers to my problem.
As far as I'm aware the second R.Y.N.O. weapon is not free, not even if you've completed the first game. I went through the Ratchet and Clank Collection in order from the first game, to the second, and then finished up the third. Each time in sequential order, the R.Y.N.O. weapon had to be saved up for and bought just like with the strongest armor. It may take more time saving up for these pieces, but once you have them you'll have that much more firepower and/or be that much more well-guarded.
(some 2013 updates for the Ratchet and Clank Collection)
1. In the first game, you need to beat the race at Kalebo III. Once you beat the race, you become official spokesmen for Gadgetron (watch the cutscene). However, the employee discount isn't immediate. Have at least one save file at all times where you are past Kalebo III but not yet beaten Drek at the end. Once you beat Drek, it resets the scenario and you are no longer "employees" even though you beat the game. At least that's how it was in the original game. I wouldn't take the chance in the Ratchet and Clank Collection, since it was such an obscure bug.
2. In Going Commando, there is a Gadgetron vendor on Planet Barlow. When you get there, the game will check the save files to see if you're a Gadgetron employee (see above). If you are, you will get most of the original Gadgetron weapons for free or cheap (I forget exactly). There are a total of 5 free/cheap weapons. These are weak weapons compared to the ones you will find in Going Commando. But there is also that 6th weapon, the RYNO II.
3. The other Gadgetron weapons are the exact same as the original weapons except that they have a "Mega upgrade" when you go to Challenge Mode. But then the enemies are tougher, so it just about balances out. However, in the first game remember that the RYNO was an illegal weapon. The RYNO II is similar to the RYNO in a few ways, but it is definitely a different weapon, possibly legal now. They didn't go too far into the back story. It's just a weapon you can buy on Barlow, and worth every bolt.
4. The starship modifications and weapons modifications are "illegal" in Going Commando, so the sneaky vendor will appear here and there selling them to you. The only illegal upgrade you can get for the RYNO II is the lock-on mod. It will make short work of the Boss Protopet, as well as Megapede in the arena battles. Sometimes Megapede flies around above you, but if he's locked in, the RYNO II will shoot straight up to kill him.
5. Be careful with your Platinum Bolts. Don't waste them all on upgrades for the loser guns. Save some for the really good guns like the RYNO II. If you're missing one P Bolt, don't let that be the one that will prevent you from getting the lock-on mod for the RYNO.
6. Another thing you may have overlooked is the Meteor Gun. When you get the lock-on mod for the Meteor Gun, it becomes a poor man's RYNO II. It's pretty powerful and may be enough to take down that Boss Protopet.
7. There is another expensive weapon called the Zodiac. It's nowhere near as good as it claims to be. Buy this last. It should be the very last thing you buy. The Clank Zapper is also a crap weapon. Once you upgrade it, you might never use it again. It's pathetic and slow.
8. Once you start Challenge Mode (meaning you beat the game and are playing it again), you get to keep all your weapons and weapon upgrades. Don't be alarmed when they don't show up in your Quick Select. Also, bolt values go up drastically. The base is higher, and you get a bolt multiplier that goes as high as 20x. All your enemies are worth 20 times as many bolts. Also, the races, space battles, and arena battles all go up in value. Seriously, they just throw bolts at you. It's crazy. So you will have no problem buying the RYNO II after a while. You won't need a bolt glitch to afford it, like you do in the first game.
9. There are many other things that cost lots of bolts, like the upgrades to Mega weapons. Upgrade the weakest ones first, as they are able to kill the enemies on Oozla and Endako. They are nearly useless at the end of the game.
10. When you get to Challenge Mode, make sure you have the RYNO II by the time you get to Planet Grelbin. If you use the shield and RYNO II together, you can walk through the planet fairly easily. The Y.E.T.I.s die with one shot. Wait for them to pop out and land before shooting. The ice dragons die with 4 shots. Make sure you don't rapid-fire them. Shot (pause) shot (pause) shot (pause) shot. Dead. If you can maintain a 20x bolt multiplier for most of the level, (very easy to do) the enemies are worth lots and lots of bolts. Some people try to blast past them with the Charge Boots. I go and kill every one of them. You will literally get millions of bolts doing this, plus there's a Trophy/Skill Point for getting all the Moonstones.
11. On Grelbin, make sure you have less than 60 RYNO II ammo before breaking open an ammo box. Sometimes they have two ammo in there, and there is 20 ammo each. If you have 79 ammo and you break a box with two ammo clips, the first one will be worth 20 and the second will be worth 1. So don't do it. When you totally run out of ammo, make sure you have a clean path back to the ship. I usually work from the left side of the screen up and down, and work to the right. When you're out, come back for ammo. On the first try, remember there are two ammo boxes on the ground near the ship. Then buy some more. As expensive as the RYNO II ammo is, it is still amazingly cheap compared to the 1600 or so bolts you get for killing a "fresh" Y.E.T.I. Now go back out and kill some more.
12. Don't be a goof and use other weapons. You might get 4 Plasma Storm ammo for breaking a box, as opposed to 20 RYNO II ammo. 20 RYNO II ammo equates to 20 dead Y.E.T.I.s. Nothing else does. So only use the RYNO II.
13. I mentioned "fresh" enemies. The game knows the difference between a new enemy and one you already killed. On Grelbin, if you already killed an enemy (like the ones in the main circular area), they will be worth fewer bolts if you die or come back to the planet, and have to kill them again. They are also worth fewer nano upgrade points. However, on Grelbin, it is still worth killing the enemies again, because they are still worth about 600 bolts as opposed to the 50 bolts it costs per RYNO II ammo.
14. Once you beat the game and come back, all the enemies in the game are considered "fresh" again.