Right - this is a one shot guide on dealing with Hyper Bosses.

Hyper Bosses are essentially... well , plotline characters using suits which is 3x stronger than usual.
One full blast from these fellas can send a chunk of your HP into the... well... oblivion.

Here are some tips before attempting some of these ridiculous missions

Unlock the "No Limits to Upgrade of MS"

Well - you'd pretty much unlock this the moment you've finished all the main story missions.
Essentially , you can upgrade a MS BEYOND their normal limits - so you can even upgrade a ZAKU II to ridiculous power levels. ( Funniy enough , my friend started panicking when he noticed my ZAKU II S Char Custom is 3 x faster than usual... )
However , upgrading requires A LOT of money and you'd need to use a MS 10 times in order to unlock this feat for that suit.
You may think that this is "cheating" but once you get exposed to teamups like the Celestial Being - you'd know this isn't cheating.

Rafflesia Mobile Armor

Rafflesia is the flower-shaped Mobile Armor from F91 and it's easily the strongest Mobile Armor in the game.
If you apply the above point to this Mobile Armor , most Hyper Boss fights should be a drift in the park.
But if you desire a challenge , I advice using the 00 Gundam for your battles.

Train your pilots

Make sure all three pilots are FULLY TRAINED with the "No Limits to Pilot" feat activated.
Also , equip Passive Skills which would hasten the process of SP regeneration and skills which would save your arse - like HP regeneration.

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Right , now for the actual guide in question.

Zeta / ZZ Teamups

The Zeta and Double Zeta enemies are actually pretty easy to handle. If you don't get careless and get yourself caught in an undesirable situation anyway.
Little info is needed for this one , just go an kick some arse.
However , take note that one of the missions would have a pilot handling the Mega Rider. Take out that unit first because the Mega Rider can deal some SERIOUS damage to your Depot.
Better still , take that Mega Rider and send back the beams to your foe.

Freedom x Justice

I seriously hate fighting against Seed pilots.
Note that Freedom and Justice would spend most of the time wisping about the air so it's best if you use a Mobile Suit which can bring them down in a matter of seconds for a healthy melee combo.
Melee-wise , Freedom and Justice shouldn't pose a threat unless your a really horrible melee fighter.
Since their defence is pretty low , use an SPA the moment you get the chance - it ought to either finish them off or send 1/2 of their HP into the oblivion.

Victory / V2 Assault Buster

Victory Gundam's battle is pretty straightforward - the main issue is V2 Assault Buster.
Uso is a pretty powerful pilot. He have ridiculous stats and his equipped skills allow him to regenerate 80%-90% of his HP if you don't finish him off with a powerful attack when his HP is low enough.
V2 Assault Buster is as annoying as Freedom and Justice , since he have the tendency to fly around like a bee - a really powerful bee which sends beams from the skies.
Remember that beam weapons are not effective against the V2 owing to it's shield so use Mobile Suits which is either powerful at melee or have a Bazooka in hand.
Note that the V2 Assault Buster does enjoy spamming his SPA skills once every few minutes so watch it when he glows red.

Hi-Nu Gundam

Right - the Hi-Nu , one of the battles , other than Uso's , which I find incredibly annoying.
Amuro doesn't have any annoying skills like Uso but the damage dished out by the Hi-Nu can be really ever so annoying.
A full array of attacks can take out a chunk so avoid those funnels and beams at all costs.
I recommend using Throne Zwei ( A Rank Gundam with a sword in 00 ) and spam your melee attacks on him until he... well , wither and dies.

Providence Gundam

Providence was surprisingly tough considering that he wasn't a "unique suit" and that he is alone.
The main issue at hand is his beam MG and his funnels ( Or rather , Dragoons )
Essentially , dodging is the key to this mission , since a Dragoon can easily loop to your back and send a beam when your guarding the front , though you DO have to block ( From a distance ) when Crusade decides to use an SPA attack.
It's recommended that you use a Mobile Suit with strong ranged capabilities since it isn't really that nice to come up close and personal with Crusade.

Mobile Armor Guide

I'll lump all the MA into a single guide since their all essentially big , nasty and yes , ridiculously nasty.
Essentially , fighting against an MA means you'd need A LOT of firepower so it's highly recommeded that you use units like Kyrios ( Gundam with bombs of 00 ) and have Virtue as your teammate.
Remember that it's best to keep your distance from these fellas since a clean swoop from them means your demise.
Oh yes , some MA like the METEOR , Orchis attachment and the GN-Armor features a little more speed than usual - so seriously , use Kyrios for these missions.
As a side-note , most U.C Mobile Armor have beam resistance - though if Virtue manages to blast away the shields , things would become easier.

Famitsu Fortress
This mission can be unlocked by LOSING in every single FIRST mission of every faction of every single Faction of every single timeline.
Essentially , this fortress features a Boss Rush - of which you must face every single Gundam in the 00 series in seperate chambers , as well as some minor goons here and there.
Don't worry too much about it , this mission is pretty easy if you can take down the V2 AB or the Hi-Nu.

Celestial Being

The mission which has brought much tears and pain into the players of this game.
In this mission , you fight against FOUR Gundam. Exia , Dynames , Kyrios and Virtue.
This mission isn't exactly pretty. Virtue would send a colossus killer beam in your direction ( Or your base's ) , Dynames would snipe you from a distance , Kyrios would... well , send missles in your face and Exia would fire beams at you and throw his Daggers.
Essentially , the first few targets to take out would be Virtue and Dynames, Then Kyrios and finally Exia.
Try not to get hitted ( Which is impossible ) and try to have your battles centered around your mothership.
Spam your SPA attacks on every given opportunity and you would NOT like it if this battle drags out for too long.
Also , most importantly , focus on a target at a time.

Trinity

The Trinity Gundam is more annoying than challenging. It is advisable that you finish of Nena Trinity first since her SPA involves the disabling of your radar - and that isn't going to be pretty since you can't hit your enemies and the jammer can drain your HP as well.
The key point here is - finish off Nena when her HP drops to a certain level ( When it's a bit orange and all ) with a powerful SPA attack. Make sure you DO finish her off - otherwise , be prepared to suffer minutes worth of hiding , dodging and yes , praying.

Penelope and Xi Gundam

....... One of the most disappointing battles EVER.
Seriously , the Penelope and Xi Gundam are like the walk in the park.
Their weak thrusters and bulky nature makes them easy to hit and easy to topple with strong attacks.
My battles with them always lasts a couple of minutes.
However , remember that they have some pretty serious firepower so stay back and dodge.