All the clones move in and live within Khan’s tower and secret base of operations for the Turbokat2 and his vehicles.  All of the characters from the Mainstream series had roles in my notes, but that is entirely up to you.  Feral’s clone was introduced to the family and once they accepted his origin, was accepted as a member without concern.  You may have to reread my stories on the Clone Saga to figure out who was connected to whom sexually.  White takes on the name of Bengalis Khan and is ‘officially’ Khan’s half brother.  Khan has three specially trained scientists who built the Tkat2 and additional equipment with the other clones.  A black furred feline named Ronrineko, a white with siamese patterns named Kajo, and a solid grey feline named Gurei.   In my original plan Gurei turns out to be a traitor, though not by choice.  He was being controlled by the Gendine Corporation.

 Plot wise, this much was laid out:

Gendine was a front for an organization known only as Seven.  Seven turns out to be a group of aliens led by another named Karthis.  NONE of these aliens are the same as the one that made the clones.  The Seven are in fact a interdimensional race of conquerers who have targeted this dimension.  They did not have cloning technology and no longer did after the alien destroyed the lab after confessing in the fifth part of the Clone Saga.  Karthis had no idea that the being who gave and the stole back the cloning tech was another alien.  He also didn’t realize the alien planned to destroy him.

The alien in question is in fact a semi energy based entity that turns out to be the dopleganger of Jake Clawson from a dimension Karthis and the Seven nearly destroyed.  It turns out that the hightened sexual energy of the clones was not an accident but was deliberate.  Each orgasm resulted in a small form of energy that was released and then stored within the clones.  The Jake Alien needs this energy to save his mate’s life, Chance’s dopleganger.  The Chance alien was critically injured in Jake Alien’s dimension in the final battle to stop Karthis.  But Karthis and the seven, simply left, they were not defeated.  Jake Alien came to the SK universe to destroy Karthis and the Seven and find a way to save Chance Alien.  He deliberately created the clones as a means of defeating Karthis, knowing a dozen Swat Kats stood a greater chance than 4.  The energy collectors in the clones were designed as a last ditch effort to save his mate.  He planned to tell everyone the truth when they were ready to confront Karthis. 

 Karthis is a power monger who delights in tormenting others by controlling them, especially sexually.  (This could fit in with your plot idea about the agency.)  But when Karthis gets bored, his victims often disappear.  He is fascinated by White, Khan’s clone, and is determined to own him.  The pklot planned to have White captured and turned traitor the same was as the scientist through mind contrlling nanites.  But the scientist figures out a way to defeat his nanites and cures himself and White.  White becomes a double agent pretending to spy on the SK’s while in fact secretly collecting intelligence on Karthis and the Seven.  The scientist is so guilty over his betrayal that he plans to kill himself and is stopped by One of the kats who talk him out of it in order to redeam his honor.

 Sexuality: 

The plan was for a heavy and erotic series with numerous sexual ideas and combinations, not the least of which would be individuals having sex with their own clones or with two or more of the same feline.  But also planned to include more on Peter the one armed assistant who was one of Khan’s former lovers.  (Note, planned to involve him in combat with a cybernetic arm.)  With the hightened sexual energies of the clones, it was safe to assume sex happened everywhere at the drop of a hat.  The scientists though were all planned to be straight so someone might get some work done.  :)With the six clones I made and the ones you indicated that is a lot of males on top of the original 4, Peter, and if you want to bring in Max (Ferals’ younger brother) and his mate Jacob.  Jacob still has the identity Thomas within him and can still access the MadKat powers though they are far weaker.  

Swat Kats: Clone Saga

Cheshires:

An extradimensional species of alien kat, long since evolved past the
need for females. Nigh-immortal, they reproduce through a complex
system of selective hybrid parthenogenesis, "spawning" near-perfect
duplicates of any male they have sexual relations with (or can get a
hold of the genetic material of) and/or a perfect "hybrid" if two or
more males they have similar contact with. Their primary form of
communication is a form of "sexual empathy"; similar to how normal
kats can get aroused by being in close proximity to another kat
getting off, the Cheshires can "feel" the other person's arousal, and
share theirs with anyone else they're close to. Unfortunately, some
members of their species realized they could control the "clones" they
spawned through that connection, especially if the kats they're cloned
from are weak-willed and sexually starved, and soon set about
conquering various worlds to feed their newfound lust for sexual
domination. A civil war broke out soon afterwards, but the opposition
to this new faction's rule were quickly subjugated or wiped out, and
now there are only a handful left of the resistance.

The new faction, calling themselves the "Sexivalence", is controlled
by a group of six unknown but immensely powerful Cheshires, lorded
over by a seventh one known as Karthis. Though not sadistic in the
sense that they revel in the pain and suffering of others (or have a
fetish for blood, gore, or torture), they do have a rather apathetic
attitude towards those under their thrall, using them as little more
than sex toys and "feeding" on their arousal, keeping them in line
with a psychological dependency on their sex. The "originals" (the
kats used by the Sexivalence to create their clone slaves) are
harvested and kept as concubines, while the clones "replace" the
originals and serve as warriors, sleeper agents, and spies, preparing
the way for more "recruits". Those who have outlived their usefulness
or that the Sexivalence are simply "bored" with are literally fucked
into oblivion,  a final orgy that disintegrates the victim into a
semen-like substance upon their last, monstrous orgasm, the residue
absorbed into the system of the Sexivalence so a new, "better" clone
can be made.

Because of the sheer power and sexual prevalence of the Sexivalence,
the resistance needed powerful warriors used to both facing formidable
and unusual foes and sexually-insatiable partners. Thus, they settled
on the Swat Kats, Kahn, Feral, Steele, and Bagheera; not only have
they taken on the likes of Dark Kat, Mad Kat, Dr. Viper and the
Pastmaster, but their sexual appetites for one-another is second to
none in their world. Also, they are the only "mortal" beings that the
resistance has found that has the same kind of innate sexual empathy
that the Cheshires as a whole have; unlike that of the Cheshires,
though (which have been honed into a conscious, deliberate act that
can be twisted and controlled to its user's will), the Kats' empathy
is more "pure" - completely instinctual, independent of the whims of
conscious desire, and freely accessible – meaning the Kats have a
natural defense against the empathic sexual attacks of the
Sexivalence. By cloning the Kats and enhancing their "pure" sexual
empathy, the resistance gave themselves the best soldiers they could
ever hope for in their fight against the Sexivalence.

Dark Kat, Dr. Viper, and Madkat:

But the Sexivalence have powerful warriors of their own in Megakat
City. Hearing about the incident at Gendine, the kat-serpent hybrid
Dr. Viper began looking into how the clones were created and by who,
hoping to use the technology that created them to develop an
invincible army of Viper clones. Intrigued, the Sexivalence sent one
of their avatars to "recruit" the villain to their cause, opening him
to a literal orgy of sexual and biological experimentation that he
could only dream of. He'll eventually become part of their "harem",
unbeknown to him, but for the moment they see his experience with his
world's populace's physiology and mechanics as an asset to their
plans.

Meanwhile, the mad would-be dictator Dark Kat also catches wind of the
Sexivalence's presence in the Kats' dimension, and also schemes to
join them, but for different reasons: Decades ago, Dark Kat was
Andromalius Feral, great granduncle of Ulysses Feral and once-lord
over a good portion of what is now Megakat City. A stern and harsh
man, with a sexually dominant appetite to rival even the Sexivalence,
he was eventually kicked out of the Feral clan when they learned he
was studying the dark practices of the clans' patron deities. Hoping
to gain full favor with the darkest of those deities, the sexual
"demon" Sensuris, he engaged in many sexual acts that were
borderline-forbidden in the clan as part of an ongoing ritual to grant
himself more power and prestige with his master. He eventually
succeeded, for a time, when he found a ritual that would allow him to
steal the youth from a family member through an ultimately-fatal
non-stop orgy, seducing his firstborn nephew and grandnephew with the
promise of "sex beyond their wildest dreams" into willingly becoming
the needed sacrifice. When Feral was born, Andromalius targeted him
for the same, and for a great while, it worked, until Feral joined the
Enforcers and began a sadly untimely love affair with a fellow cadet.
Threatened with the loss of his sacrifice, Andromalius used his
contacts to set up the aborted sniper attack on him at the Gay Pride
parade, leaving just enough evidence to hint at another cadet, known
to be a staunch homophobe, being the culprit. He hoped that the attack
and false accusation would scare Feral into breaking off the
relationship with the cadet and leave him free for the (sexual)
slaughter, but the plan backfired on him, and Feral grew closer to the
cadet, leaving Andromalius to first don the garb of Dark Kat (in
reality the robes and tribal mask needed for the final ritual) and
attack the cadet directly, killing him in a brutal rape. This was the
cause of Feral's undying hatred for Dark Kat, never knowing that he
was the same man he had been the progeny of; ironically, Dark Kat
never knew that Feral had planned for his new love to meet with him,
netting him two young, strong male kats for the ritual which would've
effectively doubled his power.

Now, though, Dark Kat believes that the Sexivalence are the servants
of his partron demon, their form somewhat similar to what the dark
texts depict them as. As such, he is convinced they have come to grant
his wish to become one of them and help welcome them in to envelop the
world. Much like their team-up with Viper, the Sexivalence see Dark
Kat's contributions of his mystical knowledge and technological genius
as assets to their conquest of the Kat's dimension, but unlike Viper,
they find their similar goals to be refreshing enough to maybe
"ascend" him – or at least his regenerated clone – to a higher
position in their armies than Viper. (Note: Dark Kat, like the
Sexivalence, aren't into gory sadism; the rituals and spells he uses
to kill his intended victims essentially drains them of sexual energy
like a vampire or incubus, essentially screwing them to death - the
medics will usually determine his victims dying of a sexually-induced
heart attack or neural failure due to sexual overstimulation.)

Mad Kat is a different story; while he cares deeply for his new host
and their husband, he knows that there will come a time where he and
Jacob will have to separate, lest their joining create an irreparable
barrier to Jacob's and Max's relationship. However, after almost five
years of their joining, Mad Kat – Thomas – is loathe to move on,
wishing to experience life as he should have before his untimely
death. When he, Jacob, and Max learn about the clones and of the
Cheshire resistance's part in their creation, Thomas believes he's
found the answer: once the war is over, have one of the resistance
members create a clone in which he could transfer his spirit into,
thus allowing him to live normally without disrupting Jacob and Max's
lives. However, before he could ask about the feasibility of such a
plan,  he and Jacob are captured by the Sexivalence, tipped off to Mad
Kat's power by Dark Kat. Using a sexual probe, the Sexivalence finds
out about Thomas' secret desire, and proposes to fulfill that wish if
he would join them. Despite his unsurety, Thomas ultimately refuses
the offer, but his moment of uncertainty allows the Sexivalence to
gain a genetic sample from him and Jacob, creating a clone of Jacob
with trace amounts of Thomas' power, effectively giving them a "voodoo
doll" through which they can manipulate the duo without their consent;
Thomas and Jacob are rescued before the clone is created, so they have
no idea of its existence, or that they are unwilling moles for the
enemy.

Gendine:

Gendine, the research business that was a front for the Cheshire
resistance's cloning of the Kats, was by and large uninvolved with the
Cheshires or their war; Gendine was a lucrative genetics firm on their
own, specializing in stem-cell research and gene therapy. However, by
the time the Cheshire that cloned the Kats (named Zarthscer,
pronounced "Zarths-chur") came around, they were about ready to go out
of business due to a lack of funding and low stocks; his arrival and
commandeering of their operations boosted their image substantially,
bringing them out of the hole they were in. Although they were left
without the secrets of perfect cloning when Zarthscer left, their
study of the clones he did make, along with the scant data he left
them, did give them a significant discovery that they would spend
years trying to figure out: the gene sequence for a "super STD",
harmless to normal Kats (and, during initial tests, proved to be an
effective panacea against all of the regular STDs in the world), but
extremely fatal to Cheshires and their clones – a backup plan should
the Swat Kats and their clones fail. Why the resistance hadn't used it
earlier is explained late in the series: first, it's still in the
experimental stage, and thus there's no guarantee that it would work
100%, and second, it requires a virulent and equally-fatal STD to be
used as a template (hence why it seems to "cure" the other STDs out
there; it actually merges with and mutates it into a strain of itself
that is harmless to normal Kats but deadly to Cheshires), and not only
are Cheshire biology highly resistant to most forms of "normal" STDs,
but most of the worlds conquered by the Sexivalence are those who had
for the most part eradicated and/or cured all their common maladies,
including STDs. Gendine has since come under the auspices of the
Federal Sexual Investigations Bureau due to the incident with
Zarthscer, and are naturally targeted by the Sexivalence once they
learn of the STD.

Hard Drive and Peter:

Hard Drive's involvement with the Cheshire incident is a long and
complicated one, involving another close ally to the Kats and their
clones, Peter. Long ago, the two were college buddies at MKTI. Hard
Drive, then going by the name of Marz Raikou, was a child prodigy
majoring in electrical science, while Peter was studying software
development and programming. The two shared a close bond, becoming
good friends and sensational lovers; Peter was always amazed at the
kind of electronic sexual toys Marz would develop. However, their
secret romance soon became known to the headmaster of the institute, a
vicious and extremely homophobic kat who was jealous of the technical
brilliance of the two students. Knowing that the two kats had a thing
for electrostim, and would often fool around late at night in one of
the institutes's labs using the school's Tesla Coil for some kinky
sex, the headmaster rigged the machine to overload during one such
night. The result was devastating; Marz was hit with the full force of
the overload,  while Peter, in an attempt to pull his friend away from
the machine, suffered severe neural damage to his right arm, requiring
it to be amputated later. Fortunately, campus security found them and
took them to the hospital, but the damage was already done; Peter was
left without an arm, and Marz was stuck in a coma for years.

Eventually, Peter moved on with his life, becoming the personal
secretary of Shere Kahn, while Marz woke up a few years afterwards,
forever changed by the accident; his bioelectrical field had been
altered, giving him the powers he would eventually develop as Hard
Drive. He soon learned, however, that everything has a price; like a
battery, his own personal electrical field would discharge without a
way of recharging himself, leading to his untimely death. As a result,
he utilized his technical expertise to develop his Surge Coat, a
combination pacemaker and power regulation suit, allowing him to focus
his new abilities while keeping his bioelectrical field stable. His
first act afterwards was to hunt down and kill the headmaster, raping
him with the same electrical power that he tried to use to kill Marz
and Peter. But while he also tracked down his former love in the
process, Marz, now Hard Drive, decided not to renew the relationship;
he didn't want Peter to see him as he was now, and besides, his
condition was still unstable even with the Surge Coat, meaning he
needed to find a way to restore himself to semi-normalcy.

At first, he got the money for his experiments by using his powers to
tap into ATMs, but soon went to being a hired thief when he realized
his powers could be put to better use acquiring goods and information
for others. By the time he started regularly encountering the Swat
Kats, he had acquired enough funds and biotech information to create a
smaller, more internal regulator that stabilized his condition
considerably, allowing him to go for quite a while without his Surge
Coat. However, as more and more of his robberies were thwarted by the
Kats, his hardware stared becoming outdated and error-prone, leaving
him with little choice but to hit the newly-transferred Megakat City
branch of Kahn Industries. There, he was quickly captured by Kahn's
men, and reunited with his long-lost love. The two fought, soon
afterwards, Peter bitter and spiteful over Hard Drive's new life and
refusal to seek him out for help. They reconciled, though, and with a
little help, Hard Drive was given a full pardon and enough medical and
technological aide to fully stabilize condition...in return for his
help in developing the equipment Kahn had planned for his mate, Feral,
to become Swat Kats themselves.

Results of the War:
The war, while long and damaging to the city, shockingly resulted in very little actual casualties; among the few who lost their lives were Mayor Manx, who sacrificed his life to take out a few of the Sexivalence. Several male Kats were captured by the Sexivalence, but were rescued. The war also blew the cover of the Swat Kats to the city, as well as exposed Khan's and Feral's relationship; the latter suffered little ill effects from the reveal after the war, while the former lead to the Swat Kats' official sanction by the Enforcers as their go-to task force for dealing with high-level metakats that the Enforcers cannot handle.

The biggest result, by far, of the war was the revelation of Zarthscer and the Sexivalence: they, as well as the Cheshires as a whole, were alternate dimension versions of Megakat City's populace, with Zarthscer and the Sexivalence being dopplegangers of the Swat Kats and their friends, as well as their main enemies Dark Kat and Dr. Viper. In a twist, however, the Swat Kats clones were part of the Sexivalence, puppet controllers manipulated by Karthis, the Dark Kat opposite, while Zarthscer was Dr. Viper's counterpart, seeking to stop Karthis – his mate – and put an end to the atrocities they had committed. As reluctantly revealed by Zarthscer, the tale about his people naturally evolving out of their need for females to reproduce was a lie; he had actually developed a horrible plague that would kill off all females in the city, and mutate all males into immortal servants. With his mate's help, he managed to overpower both the Swat Kats and the Enforcers long enough to release the virus. With the world now theirs, the couple was satisfied with their success, spending the next couple of centuries enjoying their new empire. However, Karthis started to tire of it all and – using their version of the Pastmaster's time-warping clock – found a way to observe and then enter alternate timelines and universes, determined to gain new sexual experiences by conquering those, as well. At first, Zarthscer was all for it, and eagerly joined his mate in their transdimensional conquest, but eventually, Zarthscer began to tire of that, noting with sadness that – with each world they conquered – Karthis' growing obsession slowly began whittling away what had made Zarthscer fall in love with him, in the first place.

It was Zarthscer, in secret as to not alert Karthis that his mate was behind it, who started the resistance, freeing the original inhabitants of each world (or their clones, if the originals were already dead) and relocating them in their place in space and time. The “super-STD” he developed was in reality an altered version of the original virus he used to conquer his own Megakat City, developed specifically to disrupt Karthis' control and ultimately kill all members of their species (while simultaneously mutating the Katizens of our Megakat City into a more humane, free-willed replacement to Zarthscer and his kind, though the Swat Kats and their allies didn't know about it, at the time, and the process was deliberately slowed so they could avoid the problems Zarthscer's people ran into, when it does happen). It was a long and arduous task, one that seemed to be ultimately futile come war's end; Karthis proved too strong for the Swat Kats to handle, and with our Dr. Viper's help, managed to defeat the super-STD Zarthscer had left Gendine. In one last ditch effort, Zarthscer pounced Karthis in a vicious sexual embrace, using that moment of surprise to smash the Pastmaster's watch, pulling them, the Sexivalence, and our version of Dr. Viper and Dark Kat back into their own dimension and trapping them there for all eternity.

After the war, the others went on their lives, though with a little twist; Thomas had finally gotten his own body, becoming a stripper alongside Feral, and agreed to a surprise offer by Max and Jacob to begin an official menage a trois with them. Hard Drive and Peter were married in their own little ceremony. However, even more interesting, was the gift that Zarthscer had left behind: clones of our Dr. Viper and Dark Kat, created by the Sexivalence in case the duo decided to turn against them. Although apprehensive, Feral's family took the clones in with open arms, keeping them safe and developing their lack of social skills along the way. However, they soon learned that the Dark Kat clone, Darkie, had discovered his predecessor's old headquarters (the ritual grounds for his dark sorceries) and – more disturbing – his notes and scrolls describing the dark rituals he had performed. It was feared that history would repeat itself, and the Feral clan urged Ulysses to keep an eye on the new clones. Fortunately, their fears were unfounded; Darkie and Saiger (the Dr. Viper clone), while heavily into BDSM, had no desire to continue their predecessors' legacy, only using the rituals as inspiration for their playtime; in fact, Darkie himself was repulsed by some of the things Dark Kat had done. After discovering Dark Kat's vast hidden fortune, and deciding it would be best used in Darkie's hands, Feral agreed to help them – with supervision – develop Dark Kat's old fortress and ritual grounds into a very successful gothic-themed BDSM club.