2001: A Space-Time Odyssey

yes, but Secret-Projects focus on more un unbuild Aerospace project, not there use in Alternate History...

1 - R-9 vs R-16

Mitrofan Nedelin played a key role in ushering in the space age by concluding that rockets were the ideal means to deliver a nuclear warhead to enemy instead of bombers and ordered Sergei Korolev to develop the massive R-7 ICBM.
But this rocket and its derivatives, was powerful enough to launch Sputnik and Vostok manned space vehicles into orbit enabling the USSR to beat the US to space. but it was never an effective ICBM!
For Military purposes however, a new ICBM was necessary.
One that could be launched quickly after the go ahead, one that would be useful in retaliation against an American first strike.
So the Soviet Strategic Rocket Force wanted a better, usable ICBM launcher they could use from protective Silos.

With the success of first tactical missile using storable fuels, it became obvious the new generation ICBM have use them
So Milhail Yangel OKB-589 ordered the development of the R-16 using Toxic nitric acid and UDMH fuel.
But Korolev abhorred those fuels would be "playing with devil" and prefer cleaner Liquid oxygen and Kerosine.
He got permission to build a backup system in case the R-16 project failed: The R-9.
Actually Gluchko's OKB-456 was to build rocket engines for R-16 and R-9,
But Korolev hated him[1] and refused his offer, using his growing influence to instead have team up with Kuznetsov OKB-276 for engines.

Despite pressure to perform all safety tests before October 7th (the day of the Bolshevik revolution)
The vehicle thuroughly tested even after the date, the last thing Nedeplin needed was a failed launch[2]
Luckily all went well as the rocket soared into the sky. While the launch was not without it's faults (comming somewhat short of the intended range)
The success was more than any of the hundreds of engineers had hoped for.

While the R-16 R&D went well, the R-9 experienced problems with it’s NK-9 engines.
OKB-276 just start to build rocket engine and had not experience like it rival OKB-456, what let to violent explosion on test stand.
On April 9, 1961, the first R-9 made test launch. 54 second into flight a fire broke out in engine Nr. 4 leading to the destruction of the R-9
The second test launch in May ended in a disaster as engine Nr. 6 exploded 20 second after launch.
OKB-1 started to check the delivery NK-9 engines and found faulty welds, metal shavings in turbo pump, fuel lines and Injector-plates.
Kuznetsov made his best to increase the production standards and to push for better quality control on rocket engines.
And with success, on October 25, 1961. The third R-9 launch went good following which the R-9 started a series of launches for it qualification.

By this time it was too late for the R-9 project, In same time the R-16 start make impressive results,
On August 1961 the R-16s were being deployed as operational ICBMs all along the Soviet Union
The R-16 would be used in mass for several years untill it's eventual retirement.[3]

The R-9 stay as reserve force in case, all R-16 had to be fired in case of War, were they came too close in October 1961
Final end of R-9 came on October 24 1963, with LC-70 silo disaster. A oxygen tank leak in the Silo fueling system, let to a blaze killing seven men of the launch crew.
The R-9 was pullt out of Service, Sergei Korolev accepted the failure of R-9, he was busy for moment with a important projects for Soviet Union.
The real winner of the entire R-9 ordeal was Kuznetsov's OKB-276, which with each error learned more and more how to build rockets engines and that would be quit handy for a future Korolev/Soviet Space project.[4]


NOTES:
[1] in 1938 Korolev was deliberately accused and send to gulag camp later he works as prisoner under Gluchko at OKB-16, Here became the former friends mortal rivals and enemies.

[2] The Nedelin Tragedy is famous in rocket history for being one of the worst launch failures ever. 120 people died, the program was delayed by a year, and was covered up untill 1989. here in Story the launch is successful because took more time for testing.

[3]Without the Nedelin Tragedy, the R-16 becomes a commonly deployed ICBM. With the Soviet Union more reliant on ICBMs they never need to deploy IRBMs in Cuba and the Cuban Missile crisis never happens. The results of this will become clearer later in the story

[4]Korolev was forced to work with Glushko who built the rocket engines for the R-9 rather than Kuznetsov, which lead to problems when the Kuznetsov completely inexperienced with rocket engines, was tasked with designing, building, testing and launching the NK-15 engines years later for the N-1 project.
In story with greater influence in the Soviet leadership, Korolev is able to get his way and isn't forced to cooperate with Glushko, whom Korolev hated.

Yes, do issue with the R-16 and the Nedelin Tragedy

Khrushchev took a dangerous gamble and installed IRBM on Cuba (just like NATO installed IRBM in Italy and Turkey)
But USA found the installations in Cuba too early and world was close to nuclear War.

In this TL, the R-16 works and deployed in large numbers earlier making the Cuba gamble pointless.
but that makes this world not save, what part 2 shows clearly

How do French not recognize this as being a civil aircraft.

Actually, They firer Warning shot to force the Plane to land, not knowing who was on board and why it enter Algerian airspace.


wait and see

This video give you the Mind set of Swiss around that time

There original Plan was to licence build in Swiss a 100 French Dassault Mirage IIIS (S for Switzerland)
Modified for Swiss weapons and Radar systems and for storage in aircraft caverns in the mountains, that Swiss Air Force uses as bunkers.
and of course drop a nuclear warhead on target just like it french counterpart!

So far i know had the French no idea what Swiss were planing with Mirage III as they sign the licence with them
Official there were Interceptors for Swiss Air Force...